zotero-mcp

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

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✨ Features

🧠 AI-Powered Semantic Search

• Vector-based similarity search over your entire research library (requires [semantic] extra)
• Multiple embedding models: Default (free, local), OpenAI, and Gemini
• 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
• Semantic search for conceptual and topic-based discovery

📚 Access Your Content

• Retrieve detailed metadata for any item (markdown or BibTeX export)
• Get full text content (when available)
• Look up items by BetterBibTeX citation key

📝 Work with Annotations

• Extract and search PDF annotations with page numbers
• Access Zotero's native annotations
• Create and update notes and annotations
• Extract PDF table of contents / outlines (requires [pdf] extra)

✏️ Write Operations

• Add papers by DOI with auto-fetched metadata and open-access PDF cascade (Unpaywall, arXiv, Semantic Scholar, PMC)
• Add papers by URL (arXiv, DOI links, generic webpages) or from local files
• Create and manage collections, update item metadata, batch-update tags
• Find and merge duplicate items with dry-run preview
• Hybrid mode: local reads + web API writes for local-mode users

🌐 Flexible Access Methods

• Local mode for offline access (no API key needed)
• Web API for cloud library access
• Hybrid mode: read from local Zotero, write via web API

🚀 Quick Install

Default Installation (core tools only)

The base install is lightweight — it includes search, metadata retrieval, annotations, and write operations. No ML/AI dependencies are pulled in.

Installing via uv (recommended)

uv tool install zotero-mcp-server
zotero-mcp setup  # Auto-configure (Claude Desktop supported)

Installing via pip

pip install zotero-mcp-server
zotero-mcp setup  # Auto-configure (Claude Desktop supported)

Installing via pipx

pipx install zotero-mcp-server
zotero-mcp setup  # Auto-configure (Claude Desktop supported)

Optional Extras

Heavy ML/PDF dependencies are separated into optional extras so the base install stays fast and small:

For example, with uv:

uv tool install "zotero-mcp-server[all]"    # Full install with all features
uv tool install "zotero-mcp-server[semantic]" # Just semantic search

If you only need basic library access (search, read, annotate, write), the default install with no extras is all you need.

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 (gemini-embedding-001)

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 (fast, metadata-only)
zotero-mcp update-db

# Build with full-text extraction (slower, more comprehensive)
zotero-mcp update-db --fulltext

# Use your custom zotero.sqlite path
zotero-mcp update-db --fulltext --db-path "/Your_custom_path/zotero.sqlite"

# If you have embedding conflicts or changed models, force a rebuild
zotero-mcp update-db --force-rebuild

# Check database status
zotero-mcp db-status

Example Semantic Queries in your AI assistant:

• "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)
• An MCP-compatible client (e.g., Claude Desktop, ChatGPT Developer Mode, Cherry Studio, Chorus)

For ChatGPT setup: see the Getting Started guide.

For Claude Desktop (example MCP client)

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)
• OPENAI_BASE_URL: Custom OpenAI endpoint URL (optional, for use with compatible APIs)
• GEMINI_API_KEY: Your Gemini API key (for Gemini embeddings)
• GEMINI_EMBEDDING_MODEL: Gemini model name (gemini-embedding-001)
• GEMINI_BASE_URL: Custom Gemini endpoint URL (optional, for use with compatible APIs)
• ZOTERO_DB_PATH: Custom zotero.sqlite path (optional)

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 (fast, metadata-only)
zotero-mcp update-db --fulltext             # Update with full-text extraction (comprehensive but slower)
zotero-mcp update-db --force-rebuild       # Force complete database rebuild
zotero-mcp update-db --fulltext --force-rebuild  # Rebuild with full-text extraction
zotero-mcp update-db --fulltext --db-path "your_path_to/zotero.sqlite" # Customize your zotero database path
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)

📦 Item & Collection Management Tools

• zotero_add_by_doi: Add a paper by DOI with automatic metadata and open-access PDF attachment
• zotero_add_by_url: Add a paper by URL (arXiv, DOI URLs, and general webpages)
• zotero_add_from_file: Import a local PDF or EPUB file with automatic DOI extraction
• zotero_create_collection: Create a new collection (folder/project) in your library
• zotero_search_collections: Search for collections by name to find their keys
• zotero_manage_collections: Add or remove items from collections
• zotero_update_item: Update metadata for an existing item (title, tags, abstract, date, etc.)
• zotero_find_duplicates: Find duplicate items by title and/or DOI
• zotero_merge_duplicates: Merge duplicate items with dry-run preview; consolidates all child items
• zotero_get_pdf_outline: Extract the table of contents / outline from a PDF attachment
• zotero_search_by_citation_key: Look up items by BetterBibTeX citation key (with Extra field fallback)

🧪 Testing

Unit Tests

uv run pytest tests/     # 294 tests, ~2 seconds

Integration Test Plan

A 45-point live integration test plan is included at docs/integration-test-plan.md. It's designed to be given to Claude in Claude Desktop, which will execute each test against your real Zotero library. Tests cover all tools, PDF attachment cascade, attach_mode, BetterBibTeX lookups, and multi-step showcase prompts. See the file for full instructions.

🔍 Troubleshooting

General Issues

• No results found: Ensure Zotero is running and the local API is enabled. You need to toggle on Allow other applications on this computer to communicate with Zotero in Zotero preferences.
• 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 your MCP client config (e.g., Claude Desktop)
• ChromaDB / stale embedding model errors: If you changed embedding models and see 404 errors (e.g., text-embedding-004 is not found), run zotero-mcp update-db --force-rebuild to recreate the collection with your current model. If that doesn't work, delete ~/.config/zotero-mcp/chroma_db/ and rebuild.
• Database update takes long: By default, update-db is fast (metadata-only). For comprehensive indexing with full-text, use --fulltext flag. 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
• Limited search quality: For better semantic search results, use zotero-mcp update-db --fulltext to index full-text content (requires local Zotero setup)
• 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

☕ Support

If you find Zotero MCP useful, consider buying me a coffee!

📄 License

MIT