EndNote MCP

Connect your EndNote reference library to Claude AI. Search references, read PDFs, and format citations — 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 that discuss grounded theory methodology"
"Give me the APA citation for reference #1234"
"Read pages 5-7 from that Smith et al. paper"
"List all my references about inequality from 2015-2023"

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

How It Works

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

Your references and PDF text are indexed into a local SQLite database with full-text search. Claude connects to it through the Model Context Protocol (MCP).

Requirements

EndNote 20 or 21 (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.

Commands

Command	What It Does
`endnote-mcp setup`	Interactive setup wizard
`endnote-mcp index`	Re-index after adding new references (incremental)
`endnote-mcp index --full`	Full re-index from scratch
`endnote-mcp index --skip-pdfs`	Index metadata only (fast, ~1 sec)
`endnote-mcp status`	Show index statistics
`endnote-mcp install`	Add to Claude Desktop config
`endnote-mcp serve`	Start MCP server (used by Claude Desktop automatically)

Tools Available to Claude

Tool	Description
`search_references`	Search by author, title, year, keywords, abstract (BM25 ranked)
`search_fulltext`	Search inside PDF content — find concepts, quotes, methods
`get_reference_details`	Full metadata for a reference (abstract, keywords, DOI, etc.)
`get_citation`	Format as APA 7th, Harvard, Vancouver, Chicago, or IEEE
`read_pdf_section`	Read specific pages from a PDF attachment
`list_references_by_topic`	Broad topic-based listing
`rebuild_index`	Re-index after updating your EndNote library

Adding New References

When you add new references to your EndNote library:

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

Performance

Operation	Time (4,000 references)
Metadata indexing	~1 second
PDF extraction (first time)	~1 min per 100 PDFs
PDF extraction (incremental)	Only new PDFs
Search queries	< 50 ms

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

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"

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

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 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.18617547

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.

endnote-mcp

Quick Install