EndNote MCP

Connect your EndNote reference library to Claude AI. Search references, read PDFs, format citations, find related papers, and generate bibliographies — all directly in Claude Desktop conversations.

What It Does

Once set up, you can ask Claude things like:

• "Search my library for social capital and Bourdieu"

• "Find papers about how organisations deal with uncertainty" (semantic search)

• "Find references related to paper #3844"

• "Give me the APA citation for reference #1234"

• "Generate a bibliography for references 12, 45, 78, 102"

• "Export references 12, 45, 78 as BibTeX"

• "Read pages 5-7 from that Smith et al. paper"

Claude searches your local library — nothing is uploaded to the cloud beyond the normal conversation.

Related MCP server: Claude RAG MCP Pipeline

How It Works

EndNote Library → XML Export → endnote-mcp index → SQLite Database (FTS5 + Embeddings)
                                                          ↕
                                   Claude Desktop ← MCP Server (12 tools)

Your references and PDF text are indexed into a local SQLite database with full-text search. Optionally, AI embeddings enable semantic search — finding papers by meaning, not just keywords. When semantic dependencies are installed, new references are automatically embedded during indexing. Claude connects through the Model Context Protocol (MCP).

Requirements

• EndNote 20+ (any edition)

• Claude Desktop app

• Python 3.10+

• uv (recommended) or pip

Quick Start

1. Install

# With uv (recommended)
uv tool install endnote-mcp

# Or with pip
pip install endnote-mcp

2. Export your library from EndNote

In EndNote: File → Export → choose XML format → save to a convenient location (e.g., Desktop).

3. Run the setup wizard

endnote-mcp setup

The wizard will:

• Auto-detect your XML export and PDF directory

• Create the configuration

• Index your library

• Configure Claude Desktop automatically

4. Restart Claude Desktop

Quit and reopen Claude Desktop. You'll see "EndNote Library" in your MCP connectors.

That's it. Start asking Claude about your references.

Semantic Search (Optional)

Enable meaning-based search that finds references even when they use different terminology than your query. For example, searching "how companies prepare for uncertain futures" finds papers on scenario planning and strategic foresight.

# Install semantic search dependencies
pip install endnote-mcp[semantic]

# Generate embeddings (~3 min for 4,000 references)
endnote-mcp embed

This uses the lightweight all-MiniLM-L6-v2 model locally — no API keys needed, everything stays on your machine.

Commands

Tools Available to Claude

Adding New References

When you add new references to your EndNote library:

1. Re-export XML from EndNote (overwrite the same file)

2. Either:

   • Run endnote-mcp index from a terminal, or

   • Ask Claude: "Rebuild my library index"

Indexing is incremental — it only processes new references and PDFs, not the entire library again. If semantic search is installed, new references are automatically embedded.

Performance

Configuration

Config is stored at:

• macOS: ~/Library/Application Support/endnote-mcp/config.yaml

• Windows: %APPDATA%/endnote-mcp/config.yaml

• Linux: ~/.config/endnote-mcp/config.yaml

endnote_xml: /path/to/your/library.xml
pdf_dir: /path/to/your/Library.Data/PDF
db_path: /path/to/library.db    # auto-set by setup
max_pdf_pages: 30                # max pages per read request
search_notes: false              # include the EndNote Notes field in searches

Notes fields

EndNote's Research Notes — where you keep your own summaries and judgments — is indexed and searched by default, ranked just below keywords and above the abstract.

The plain Notes field is indexed but excluded from matching, because reference managers use it as a dumping ground on import: author affiliations, email addresses, thesaurus terms. Set search_notes: true to include it. The setting takes effect immediately — no re-index needed.

Citation Styles

Five built-in styles:

• APA 7th — get_citation(rec_number=42, style="apa7")

• Harvard — style="harvard"

• Vancouver — style="vancouver"

• Chicago (Author-Date, 17th ed.) — style="chicago"

• IEEE — style="ieee"

Use get_bibliography to format multiple references at once, sorted by author or year.

BibTeX Export

Export references as BibTeX entries for use in LaTeX:

• Ask Claude: "Export references 42 and 100 as BibTeX"

• Or use the get_bibtex tool directly with comma-separated record numbers

Generates complete entries with proper entry types (@article, @book, @inproceedings, etc.), cite keys, and all available fields.

Troubleshooting

"No configuration found" — Run endnote-mcp setup

"XML file not found" — Re-export from EndNote: File → Export → XML format

"PDF not found" — Check that pdf_dir in your config points to the correct .Data/PDF directory

Search returns no results — Run endnote-mcp index to rebuild the database

Claude Desktop doesn't show the tool — Run endnote-mcp install, then restart Claude Desktop

"Semantic search is not available" — Run pip install endnote-mcp[semantic] then endnote-mcp embed

Citing This Software

If you use this tool in your research, please cite it:

Gokmen, G. (2026). EndNote MCP: Connecting EndNote Reference Libraries to Claude AI (Version 1.4.5) [Computer software]. https://doi.org/10.5281/zenodo.18617546

Or use the "Cite this repository" button on GitHub for BibTeX/APA formats.

License

AGPL-3.0 — free to use, modify, and distribute. See LICENSE for details.