
zotero-mcp
Zotero MCP: Connects your Zotero research library with Claude and other AI assistants via the Model Context Protocol to discuss papers, get summaries, analyze citations, and more.
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Zotero MCP seamlessly connects your Zotero research library with AI assistants like ChatGPT and Claude via the Model Context Protocol. It offers AI-powered semantic search, access to library content, PDF annotation extraction, and easy updates. Users can search their library, analyze citations, and get summaries, making it ideal for research tasks. The tool supports multiple embedding models, intelligent search results, and flexible access methods for both local and remote collaboration. With advanced features like semantic search and PDF annotation extraction, Zotero MCP enhances research efficiency and organization.
README:
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!
- 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
- 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
- Retrieve detailed metadata for any item
- Get full text content (when available)
- Access attachments, notes, and child items
- Extract and search PDF annotations directly
- Access Zotero's native annotations
- Create and update notes and annotations
- 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
- Local method for offline access (no API key needed)
- Web API for cloud library access
- Perfect for both local research and remote collaboration
uv tool install "git+https://github.com/54yyyu/zotero-mcp.git"
zotero-mcp setup # Auto-configure (Claude Desktop supported)
pip install git+https://github.com/54yyyu/zotero-mcp.git
zotero-mcp setup # Auto-configure (Claude Desktop supported)
To install Zotero MCP via Smithery for Claude Desktop:
npx -y @smithery/cli install @54yyyu/zotero-mcp --client claude
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
Zotero MCP now includes powerful AI-powered semantic search capabilities that let you find research based on concepts and meaning, not just keywords.
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
ortext-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
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
# 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.
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.
After installation, either:
-
Auto-configure (recommended):
zotero-mcp setup
-
Manual configuration: Add to your
claude_desktop_config.json
:{ "mcpServers": { "zotero": { "command": "zotero-mcp", "env": { "ZOTERO_LOCAL": "true" } } } }
- Start Zotero desktop (make sure local API is enabled in preferences)
- Launch Claude Desktop
- 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)
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.
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
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.)
# 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 db-status # Show database status and info
# General
zotero-mcp version # Show current version
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.
-
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
-
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
-
zotero_get_item_metadata
: Get detailed metadata (supports BibTeX export viaformat="bibtex"
) -
zotero_get_item_fulltext
: Get full text content -
zotero_get_item_children
: Get attachments and notes
-
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)
-
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
-
"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 warnings: Update to the latest version - deprecation warnings have been fixed
-
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 withzotero-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 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
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