EndNote Library Connector

by gokmengokhan

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About

Search, cite, and read PDFs from your EndNote reference library directly in Claude Desktop

Details

Author
gokmengokhan
Categories
Productivity, Other, Knowledge Base

Setup

Install EndNote Library Connector in your MCP client (Claude Desktop, Cursor, Windsurf, and others).

Repository: https://github.com/gokmengokhan/endnote-mcp

Follow the installation instructions in the repository README, then restart your MCP client.

Search, cite, and read PDFs from your EndNote reference library directly in Claude Desktop

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.

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 yourlocallibrary — nothing is uploaded to the cloud beyond the normal conversation.

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 theModel Context Protocol (MCP).

- EndNote 20+(any edition)
- Claude Desktopapp
- Python 3.10+
- uv(recommended) or pip

# With uv (recommended) uv tool install endnote-mcp # Or with pip pip install endnote-mcp

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

- Auto-detect your XML export and PDF directory
- Create the configuration
- Index your library
- Configure Claude Desktop automatically

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

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

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 lightweightall-MiniLM-L6-v2model locally — no API keys needed, everything stays on your machine.

When you add new references to your EndNote library:
- Re-export XMLfrom EndNote (overwrite the same file)
- Either:

- Runendnote-mcp indexfrom a terminal,or
- Ask Claude:"Rebuild my library index"

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

- 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

- APA 7thget_citation(rec_number=42, style="apa7")
- Harvardstyle="harvard"
- Vancouverstyle="vancouver"
- Chicago(Author-Date, 17th ed.) —style="chicago"
- IEEEstyle="ieee"

Useget_bibliographyto format multiple references at once, sorted by author or year.

Export references as BibTeX entries for use in LaTeX:

- Ask Claude:"Export references 42 and 100 as BibTeX"
- Or use theget_bibtextool directly with comma-separated record numbers

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

"No configuration found"— Runendnote-mcp setup

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

"PDF not found"— Check thatpdf_dirin your config points to the correct.Data/PDFdirectory

Search returns no results— Runendnote-mcp indexto rebuild the database

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

"Semantic search is not available"— Runpip install endnote-mcp[semantic]thenendnote-mcp embed

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.

AGPL-3.0 — free to use, modify, and distribute. SeeLICENSEfor details.

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