Zotero MCP: Your Research Library in Claude

Zotero MCP seamlessly connects your Zotero research library with Claude and other AI assistants (Cherry Studio, Cursor, etc.) via the Model Context Protocol. Discuss papers, get summaries, analyze citations, extract PDF annotations, and more!

✨ Features

🧠 AI-Powered Semantic Search

• Vector-based similarity search over your entire research library
• Multiple embedding models: Default (free), OpenAI, and Gemini options
• Intelligent results with similarity scores and contextual matching
• Auto-updating database with configurable sync schedules

🔍 Search Your Library

• Find papers, articles, and books by title, author, or content
• Perform complex searches with multiple criteria
• Browse collections, tags, and recent additions
• NEW: Semantic search for conceptual and topic-based discovery

📚 Access Your Content

• Retrieve detailed metadata for any item
• Get full text content (when available)
• Access attachments, notes, and child items

📝 Work with Annotations

• Extract and search PDF annotations directly
• Access Zotero's native annotations
• Create and update notes and annotations

🔄 Easy Updates

• Smart update system that detects your installation method (uv, pip, conda, pipx)
• Configuration preservation - all settings maintained during updates
• Version checking and automatic update notifications

🌐 Flexible Access Methods

• Local method for offline access (no API key needed)
• Web API for cloud library access
• Perfect for both local research and remote collaboration

🚀 Quick Install

Installing via Smithery

To install Zotero MCP for Claude Desktop automatically via Smithery:

npx -y @smithery/cli install @54yyyu/zotero-mcp --client claude

Manual Installation

Installing via uv

uv tool install "git+https://github.com/54yyyu/zotero-mcp.git"
zotero-mcp setup  # Auto-configure for Claude Desktop

Installing via pip

pip install git+https://github.com/54yyyu/zotero-mcp.git
zotero-mcp setup  # Auto-configure for Claude Desktop

Updating Your Installation

Keep zotero-mcp up to date with the smart update command:

# Check for updates
zotero-mcp update --check-only

# Update to latest version (preserves all configurations)
zotero-mcp update

🧠 Semantic Search

Zotero MCP now includes powerful AI-powered semantic search capabilities that let you find research based on concepts and meaning, not just keywords.

Setup Semantic Search

During setup or separately, configure semantic search:

# Configure during initial setup (recommended)
zotero-mcp setup

# Or configure semantic search separately
zotero-mcp setup --semantic-config-only

Available Embedding Models:

• Default (all-MiniLM-L6-v2): Free, runs locally, good for most use cases
• OpenAI: Better quality, requires API key (text-embedding-3-small or text-embedding-3-large)
• Gemini: Better quality, requires API key (models/text-embedding-004 or experimental models)

Update Frequency Options:

• Manual: Update only when you run zotero-mcp update-db
• Auto on startup: Update database every time the server starts
• Daily: Update once per day automatically
• Every N days: Set custom interval

Using Semantic Search

After setup, initialize your search database:

# Build the semantic search database
zotero-mcp update-db

# Check database status
zotero-mcp db-status

Example Semantic Queries in Claude:

• "Find research similar to machine learning concepts in neuroscience"
• "Papers that discuss climate change impacts on agriculture"
• "Research related to quantum computing applications"
• "Studies about social media influence on mental health"
• "Find papers conceptually similar to this abstract: [paste abstract]"

The semantic search provides similarity scores and finds papers based on conceptual understanding, not just keyword matching.

🖥️ Setup & Usage

Full documentation is available at Zotero MCP docs.

Requirements

• Python 3.10+
• Zotero 7+ (for local API with full-text access)
• Claude Desktop or compatible AI assistant

For Claude Desktop

Configuration

After installation, either:

1. Auto-configure (recommended):

   zotero-mcp setup
   

2. Manual configuration: Add to your claude_desktop_config.json:

   {
     "mcpServers": {
       "zotero": {
         "command": "zotero-mcp",
         "env": {
           "ZOTERO_LOCAL": "true"
         }
       }
     }
   }
   

Usage

1. Start Zotero desktop (make sure local API is enabled in preferences)
2. Launch Claude Desktop
3. Access the Zotero-MCP tool through Claude Desktop's tools interface

Example prompts:

• "Search my library for papers on machine learning"
• "Find recent articles I've added about climate change"
• "Summarize the key findings from my paper on quantum computing"
• "Extract all PDF annotations from my paper on neural networks"
• "Search my notes and annotations for mentions of 'reinforcement learning'"
• "Show me papers tagged '#Arm' excluding those with '#Crypt' in my library"
• "Search for papers on operating system with tag '#Arm'"
• "Export the BibTeX citation for papers on machine learning"
• "Find papers conceptually similar to deep learning in computer vision" (semantic search)
• "Research that relates to the intersection of AI and healthcare" (semantic search)
• "Papers that discuss topics similar to this abstract: [paste text]" (semantic search)

For Cherry Studio

Configuration

Go to Settings -> MCP Servers -> Edit MCP Configuration, and add the following:

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

Then click "Save".

Cherry Studio also provides a visual configuration method for general settings and tools selection.

🔧 Advanced Configuration

Using Web API Instead of Local API

For accessing your Zotero library via the web API (useful for remote setups):

zotero-mcp setup --no-local --api-key YOUR_API_KEY --library-id YOUR_LIBRARY_ID

Environment Variables

Zotero Connection:

• ZOTERO_LOCAL=true: Use the local Zotero API (default: false)
• ZOTERO_API_KEY: Your Zotero API key (for web API)
• ZOTERO_LIBRARY_ID: Your Zotero library ID (for web API)
• ZOTERO_LIBRARY_TYPE: The type of library (user or group, default: user)

Semantic Search:

• ZOTERO_EMBEDDING_MODEL: Embedding model to use (default, openai, gemini)
• OPENAI_API_KEY: Your OpenAI API key (for OpenAI embeddings)
• OPENAI_EMBEDDING_MODEL: OpenAI model name (text-embedding-3-small, text-embedding-3-large)
• GEMINI_API_KEY: Your Gemini API key (for Gemini embeddings)
• GEMINI_EMBEDDING_MODEL: Gemini model name (models/text-embedding-004, etc.)

Command-Line Options

# Run the server directly
zotero-mcp serve

# Specify transport method
zotero-mcp serve --transport stdio|streamable-http|sse

# Setup and configuration
zotero-mcp setup --help                    # Get help on setup options
zotero-mcp setup --semantic-config-only    # Configure only semantic search
zotero-mcp setup-info                      # Show installation path and config info for MCP clients

# Updates and maintenance
zotero-mcp update                          # Update to latest version
zotero-mcp update --check-only             # Check for updates without installing
zotero-mcp update --force                  # Force update even if up to date

# Semantic search database management
zotero-mcp update-db                       # Update semantic search database
zotero-mcp update-db --force-rebuild       # Force complete database rebuild
zotero-mcp db-status                       # Show database status and info

# General
zotero-mcp version                         # Show current version

📑 PDF Annotation Extraction

Zotero MCP includes advanced PDF annotation extraction capabilities:

• Direct PDF Processing: Extract annotations directly from PDF files, even if they're not yet indexed by Zotero
• Enhanced Search: Search through PDF annotations and comments
• Image Annotation Support: Extract image annotations from PDFs
• Seamless Integration: Works alongside Zotero's native annotation system

For optimal annotation extraction, it is highly recommended to install the Better BibTeX plugin for Zotero. The annotation-related functions have been primarily tested with this plugin and provide enhanced functionality when it's available.

The first time you use PDF annotation features, the necessary tools will be automatically downloaded.

📚 Available Tools

🧠 Semantic Search Tools

• zotero_semantic_search: AI-powered similarity search with embedding models
• zotero_update_search_database: Manually update the semantic search database
• zotero_get_search_database_status: Check database status and configuration

🔍 Search Tools

• zotero_search_items: Search your library by keywords
• zotero_advanced_search: Perform complex searches with multiple criteria
• zotero_get_collections: List collections
• zotero_get_collection_items: Get items in a collection
• zotero_get_tags: List all tags
• zotero_get_recent: Get recently added items
• zotero_search_by_tag: Search your library using custom tag filters

📚 Content Tools

• zotero_get_item_metadata: Get detailed metadata (supports BibTeX export via format="bibtex")
• zotero_get_item_fulltext: Get full text content
• zotero_get_item_children: Get attachments and notes

📝 Annotation & Notes Tools

• zotero_get_annotations: Get annotations (including direct PDF extraction)
• zotero_get_notes: Retrieve notes from your Zotero library
• zotero_search_notes: Search in notes and annotations (including PDF-extracted)
• zotero_create_note: Create a new note for an item (beta feature)

🔍 Troubleshooting

General Issues

• No results found: Ensure Zotero is running and the local API is enabled
• Can't connect to library: Check your API key and library ID if using web API
• Full text not available: Make sure you're using Zotero 7+ for local full-text access
• Local library limitations: Some functionality (tagging, library modifications) may not work with local JS API. Consider using web library setup for full functionality. (See the docs for more info.)
• Installation/search option switching issues: Database problems from changing install methods or search options can often be resolved with zotero-mcp update-db --force-rebuild

Semantic Search Issues

• "Missing required environment variables" when running update-db: Run zotero-mcp setup to configure your environment, or the CLI will automatically load settings from Claude Desktop config
• ChromaDB warnings: Update to the latest version - deprecation warnings have been fixed
• Database update takes long: This is normal for large libraries. Use --limit parameter for testing: zotero-mcp update-db --limit 100
• Semantic search returns no results: Ensure the database is initialized with zotero-mcp update-db and check status with zotero-mcp db-status
• OpenAI/Gemini API errors: Verify your API keys are correctly set and have sufficient credits/quota

Update Issues

• Update command fails: Check your internet connection and try zotero-mcp update --force
• Configuration lost after update: The update process preserves configs automatically, but check ~/.config/zotero-mcp/ for backup files

📄 License

MIT