Zotero Setup Guide

Zotero is your primary reference management tool for the literature review process. This guide covers essential plugins and configurations to integrate Zotero with your AI-enhanced workflow, particularly with Obsidian and Cherry Studio.

Benefits:

• Centralized reference management
• PDF annotation and extraction
• Seamless integration with Obsidian for notes
• Cloud-independent attachment syncing
• Direct API access for AI tools

1.1 download Zotero

brew install --cask zotero

wget -qO- https://github.com/retorquere/zotero-deb/releases/download/apt-get/install.sh | sudo bash
sudo apt update
sudo apt install zotero

Most users should download Zotero from the official website; it works on all platforms and handles updates automatically.

1.2 create Zotero account

1. Sign up at zotero.org/user/register
2. Sign in to Zotero desktop app
3. Enable sync (File → Preferences → Sync)
   • Note: Free tier includes 300MB storage
   • We'll set up unlimited attachment storage below

2.1 install plugin market (Zotero addons)

The plugin market gives Zotero a central place to find and install extensions.

1. Download from: GitHub - Zotero Addons
2. In Zotero: Tools → Add-ons → Install Add-on From File
3. Select the downloaded .xpi file
4. Restart Zotero
5. Access via: Tools → Zotero Addons Manager

Benefits: One-click install for other plugins, automatic updates

2.2 Better BibTeX (required)

Essential for citation key management and Obsidian integration.

Via Addon Manager:

1. Open Zotero Addons Manager
2. Search "Better BibTeX"
3. Click Install

Manual Installation:

1. Download from: retorque.re/zotero-better-bibtex
2. Tools → Add-ons → Install Add-on From File

Configuration:

1. Edit → Preferences → Better BibTeX
2. Citation keys (this is my personal preference - totally optional but recommended):
   • Pattern: [auth:lower][year]
   • Example: smith2024
   • Note on duplicates: Better BibTeX automatically adds letters (a, b, c, d) to the end when you have multiple papers from the same first author in the same year:
     • First paper: smith2024a
     • Second paper: smith2024b
     • Third paper: smith2024c
   • This keeps citation keys unique and memorable.
3. Enable: "On item change, export to" (for auto-export)

2.3 attanger - attachment management

Replaces ZotFile for Zotero - manages PDFs and cloud sync.

Installation:

1. Via Addon Manager: Search "Attanger"
2. Or download from: GitHub - Zotero Attanger

Configuration for Cloud Sync:

1. Edit → Preferences → Attanger

2. Set custom attachment location:

   /Users/[username]/Dropbox/Zotero-Attachments/
   or
   /Users/[username]/OneDrive/Zotero-Attachments/

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3. Enable: "Automatically rename attachments"

4. Rename format (this is my personal preference - works great for searching):

   {{ citationKey suffix="_" }}{{ title truncate="100" }}

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   • Creates: smith2024a_Systematic_Review_of_AI_in_Research.pdf
   • Why this format? The citation key makes PDFs easier to remember and find. The title makes files searchable on your computer, so you can match PDFs to their Zotero entries.
   • For more format options, see: Zotero File Renaming Guide

Benefits:

• Unlimited storage via your cloud service
• Organized, searchable PDF structure
• Easy to find files by citation key or title
• Access PDFs from any device

2.4 zotlit plugin for Zotero and Obsidian

ZotLit creates a two-way integration between Zotero and Obsidian. It consists of a Zotero plugin and an Obsidian plugin that work together.

A. Install ZotLit Zotero Plugin:

1. Via Addon Manager: Search for "ZotLit"
2. Or download from: GitHub - ZotLit Releases
3. Install the .xpi file and restart Zotero.

B. Install ZotLit Obsidian Plugin:

1. In Obsidian, go to Settings > Community Plugins.
2. Turn off "Safe mode".
3. Browse community plugins and search for "ZotLit".
4. Install and then enable the plugin.

C. Configuration:

1. In Obsidian's ZotLit settings:
   • Connect to the Zotero database. The plugin will usually find the database automatically.
   • Configure the template for your literature notes. A good starting point for the template is provided in the ZotLit documentation.
   • Set the folder where you want your literature notes to be created (e.g., 01-Literature-Notes/).

Usage:

• From Obsidian, open the command palette (Cmd/Ctrl+P) and search for "ZotLit".
• You can create new literature notes, insert citations, and pull annotations directly from Zotero into your Obsidian notes.

3.1 Zotero MCP server for Cherry Studio

Required for the MCP (Model Context Protocol) integration with Cherry Studio. This involves running a local server that connects Cherry Studio to your Zotero library. The server lets the AI search and interact with your research.

A. Prerequisites:

• Python 3.10+ installed on your system.
• Zotero 7+ running. The local API and full-text access below require 7 or newer.
• Better BibTeX for Zotero plugin installed.

B. Enable Zotero's Local API:

1. In Zotero, go to Edit → Preferences → Advanced → General.
2. Check the box for "Allow other applications to communicate with Zotero".
3. Note the port number (usually 23119).

C. Install and Set Up the Zotero MCP Server:

This is a command-line application that you will run from your terminal.

1. Install the server:

   • The package on PyPI is zotero-mcp-server; the command it installs is zotero-mcp.

   uv tool install "zotero-mcp-server[semantic]"

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   • The base install stays small, and the heavier dependencies live in optional extras. The semantic extra is the one that provides the embedding and vector-search machinery Step 2 configures, so install it now if you want semantic search. Use [all] instead to add PDF outline extraction and Scite citation data.

2. Initial Setup & Embedding Configuration:

   • After installation, run the interactive setup command:

   zotero-mcp setup

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   • This process asks you to choose a semantic search embedding model. You have several options, including:
     • Default: A local model that requires no API keys.
     • Gemini: Uses Google's embedding models. The setup prompts you for your Gemini API key.
     • OpenAI: Uses OpenAI's embedding models. You need an OpenAI API key.
   • Select Gemini and provide your API key when prompted to enable semantic search on your research library.

3. Build the Database:

   • To allow the MCP to search your Zotero library, you need to build its database. For the most comprehensive search, include full-text extraction:

   zotero-mcp update-db --fulltext

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D. Connect to Cherry Studio:

1. In Cherry Studio, go to Settings > MCP Servers > Edit MCP Configuration.
2. Add the following JSON configuration:

   {
     "mcpServers": {
       "zotero": {
         "name": "zotero",
         "type": "stdio",
         "isActive": true,
         "command": "zotero-mcp",
         "args": [],
         "env": {
           "ZOTERO_LOCAL": "true"
         }
       }
     }
   }

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E. Further Information:

• For an overview, advanced configuration, and troubleshooting, see the official Zotero MCP repository.

3.2 Better BibTeX API

1. Edit → Preferences → Better BibTeX → API
2. Enable: "Enable BetterBibTeX JSON-RPC"
3. This allows advanced queries from Obsidian

4.1 prerequisites

Before connecting Research Rabbit to Zotero, ensure you have:

1. Zotero web sync enabled (Edit → Preferences → Sync → logged in)
2. At least one collection with seed papers
3. A Research Rabbit account at researchrabbit.ai

4.2 connect Research Rabbit to Zotero

Step 1: Enable Zotero Web Sync (if not already done)

1. In Zotero desktop: Edit → Preferences → Sync
2. Log in with your Zotero account
3. Ensure "Sync automatically" is checked
4. Allow sync to complete before proceeding

Step 2: Import Zotero Collection to Research Rabbit

1. Log into your Research Rabbit account
2. Click "Import Zotero Collection"
3. Sign in with your Zotero credentials when prompted
4. Select the collection you want to import (e.g., "Seed Papers")
5. Assign a meaningful name in Research Rabbit
6. Click "OK" and wait for import to complete

Step 3: Verify Import

• Check that all papers imported correctly
• Match imported papers with their titles
• Note: Large collections may import partially

4.3 bi-directional sync workflow

From Zotero to Research Rabbit (Discovery):

1. Create a dedicated collection in Zotero with seed papers
2. Import this collection to Research Rabbit (as above)
3. Use Research Rabbit's citation network to discover related papers
4. Use the "Similar Papers" and "Citation Map" features

From Research Rabbit to Zotero (Curation):

1. In Research Rabbit, build your expanded collection
2. Click "Sync to Zotero" button at the bottom of the page
3. This creates or updates a collection in Zotero.
4. New papers will appear in your Zotero library

Re-syncing After Changes:

• After adding papers to either platform: Click "Re-sync with Zotero"
• This ensures both collections stay synchronized

4.4 best practices for integration

Collection Naming Strategy:

Zotero Collections:
├── Research-2025_SeedPapers          # Original seed papers
├── Research-2025_RR_Discovered       # Papers found via Research Rabbit
└── Research-2025_Final_Curated       # Final selection after human review

Recommended Workflow:

1. Start in Zotero: Import 3-5 seed papers from databases
2. Explore in Research Rabbit: Import seed collection, discover related papers
3. Curate in Zotero: Sync discoveries back, apply inclusion criteria
4. Iterate: Repeat discovery-curation cycles as needed

4.5 troubleshooting integration

Sync Not Working:

• Ensure Zotero web sync is active and up-to-date
• Try logging out/in of Research Rabbit
• Check if you're using a group library (may cause issues)
• Use personal library collections only

Partial Import Issues:

• Large collections may not import completely
• Break into smaller sub-collections (<50 papers)
• Use BibTeX export/import as fallback:
  1. In Research Rabbit: Export → BibTeX
  2. In Zotero: File → Import → select .bib file

Group Library Limitations:

• Research Rabbit may only sync with personal libraries
• Create personal collections for Research Rabbit integration
• Copy papers from group library to personal library if needed

4.6 alternative export methods

If direct sync fails, use file-based transfer:

Export from Research Rabbit:

1. Click "Export" in left sidebar
2. Choose BibTeX (.bib) format
3. Download file

Import to Zotero:

1. File → Import
2. Select the .bib file
3. Choose "Place imported items in new collection"
4. Name collection appropriately

5.1 create collections structure

My Library/
├── Systematic Review Project/
│   ├── Search Results/
│   │   ├── Database 1/
│   │   ├── Database 2/
│   │   └── Grey Literature/
│   ├── Screening/
│   │   ├── Title-Abstract/
│   │   ├── Full-Text/
│   │   └── Excluded/
│   ├── Included Studies/
│   └── Analysis/

5.2 set up tags for review stages

Create standard tags:

• #to-screen
• #screening-passed
• #full-text-review
• #included
• #excluded-reason-1 (not relevant)
• #excluded-reason-2 (wrong methodology)
• #excluded-reason-3 (duplicate)

5.3 create saved searches

1. Edit → New Saved Search
2. Examples:
   • "Needs Screening": Tag is not #screening-passed
   • "Recent AI Papers": Date Added in last 7 days AND Any field contains "AI"
   • "High Quality": Item Type is "Journal Article" AND Publication contains "Nature" OR "Science"

6.1 import from databases

For systematic reviews, use these formats:

• Web of Science: BibTeX or RIS
• Scopus: RIS or BibTeX
• PubMed: PubMed XML
• IEEE Xplore: BibTeX
• Google Scholar: Use Zotero Connector

Bulk Import Process:

1. File → Import
2. Choose file format
3. Select: "Place imported items in new collection"
4. Name: "Database Name - Date"

6.2 export for analysis

For Obsidian:

• Better BibTeX → Export Library
• Format: Better CSL JSON or Better BibTeX
• Keep updated: Check this for auto-sync

For Cherry Studio:

• Use API access (configured above)
• Or export as CSL JSON

7.1 built-in PDF reader

Zotero includes a built-in PDF reader for annotation:

1. Double-click any PDF
2. Use highlighting tools. Colors can carry meaning:
   • Yellow: Important points
   • Red: Disagree/Question
   • Green: Agree/Support
   • Blue: Methodology
   • Purple: Future research

7.2 extract annotations

1. Right-click PDF → "Add Note from Annotations"
2. Creates structured note with:
   • All highlights with page numbers
   • Your comments
   • Links back to PDF location

7.3 export annotations to Obsidian

With plugins configured:

1. Right-click → "Create Obsidian Note"
2. Annotations automatically included
3. Each highlight links back to PDF page

8.1 database backup

Your Zotero database location:

• Windows: C:\Users\[username]\Zotero
• Mac: /Users/[username]/Zotero
• Linux: /home/[username]/Zotero

Backup regularly to:

• External drive
• Cloud service (different from attachment sync)

8.2 export library backup

Monthly backup:

1. File → Export Library
2. Format: Zotero RDF (includes most metadata)
3. Include: Files and Notes
4. Save with date: Zotero-Backup-2025-09-01.rdf

Common issues

Sync conflicts

• Disable auto-sync during bulk imports
• Resolve conflicts by choosing "Use local version"
• Re-enable after import complete

Attachment not found

• Check Attanger settings
• Verify cloud folder is synced
• Tools → Manage Attachments → Convert to Linked Files

Better BibTeX slow

• Reduce citation key update frequency
• Disable "Background export"
• Pin citation keys for large libraries

API not working

• Check firewall settings
• Restart Zotero
• Verify port 23119 is not in use

Plugin compatibility

• Always check "Compatible with Zotero"
• Disable old plugins before updating
• Check GitHub issues for known problems

Keyboard shortcuts

• Cmd/Ctrl + Shift + N: New item from identifier (DOI, ISBN)
• Cmd/Ctrl + Shift + A: Add attachment
• Cmd/Ctrl + Shift + C: Copy citation
• Tab: Move between fields
• Shift + Enter: Create new creator field

Useful workflows

Adding papers from PDF

1. Drag PDF into Zotero
2. Right-click → "Retrieve Metadata for PDF"
3. Verify and correct metadata
4. Add tags for review stage

Bulk tagging

1. Select multiple items
2. Drag to tag in left panel
3. Or right-click → "Assign Tags"

Quick export to Obsidian

1. Select papers
2. Cmd/Ctrl + Shift + C (with Better BibTeX)
3. Paste in Obsidian with citations

With Obsidian

• Better BibTeX provides citation keys
• Obsidian Note plugin creates notes
• Annotations sync automatically

With Cherry Studio

• Local API enables MCP access
• Zotero MCP searches library
• Exports feed the AI knowledge base

With cloud services

• Attanger manages PDF sync
• Independent of Zotero storage
• Works with any cloud provider

By the end of this guide, you should have completed the following:

• Install Zotero
• Install all essential plugins
• Configure Better BibTeX citation keys
• Set up Attanger with cloud folder
• Enable local API access
• Create Research Rabbit account
• Test Research Rabbit-Zotero sync with seed papers
• Create collections structure
• Import 3-5 seed papers
• Test Obsidian Note creation
• Verify API at http://localhost:23119

How Do You Know It's Working?

Tool Comparison Matrix

Reference Management

AI Interfaces

Knowledge Management & Note-Taking

Academic Writing & Paper Drafting

Legend: ● Full support · ◐ Partial support or workaround · ○ Not available

With Zotero set up, the natural next step is to let an AI partner work with the library through Zotero MCP. See the Cherry Studio Setup Guide for the wiring.

External references

• Zotero Forums
• Better BibTeX Documentation
• Zotero Plugins Directory