io.github.gokmengokhan/endnote-mcp MCP Server

EndNote MCP

<!-- mcp-name: io.github.gokmengokhan/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.

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

The bundle installer below has no other prerequisites — Claude Desktop manages Python and dependencies. The CLI install path additionally needs Python 3.10+ and uv (or pip).

Install (Desktop Bundle — Recommended)

The fastest install for non-engineers. No Python or terminal required.

1. Export your library from EndNote. File → Export → choose XML format → save somewhere like Desktop.
2. Download endnote-mcp.mcpb from the latest release.
3. Double-click the .mcpb file (or in Claude Desktop: Settings → Extensions → Install Extension…).
4. In the install dialog, point Claude Desktop at:
   • Your EndNote XML file (from step 1)
   • Your PDF Attachments Folder — usually <library>.Data/PDF/ next to your .enl file, or PDF/ inside an .enlp package.
5. Click Install. Claude Desktop will start indexing your library automatically — metadata is searchable within seconds, PDF text and semantic embeddings finish in the background.

That's it. Try asking Claude "Search my library for grounded theory".

The bundle keeps its own configuration (config-mcpb.yaml), so installing it will not disturb an existing CLI setup. Both default to the same database, so if you already indexed with the CLI the bundle reuses that index rather than building a second copy.

Building the bundle yourself

Maintainers (or anyone working from source) can build it with:

bash scripts/build_mcpb.sh
# → dist/endnote-mcp.mcpb

The build is a single cross-platform .mcpb file (~36 KB). Dependencies resolve at install time via the uv runtime bundled with Claude Desktop.

The format was called DXT and used the .dxt extension until it was renamed upstream to MCPB (MCP Bundles). See modelcontextprotocol/mcpb.

Install (CLI / from PyPI)

Prefer the terminal? This path gives you the endnote-mcp CLI for indexing and embedding.

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.

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

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 index --embed	Re-index and generate embeddings
endnote-mcp embed	Generate semantic search embeddings
endnote-mcp embed --full	Regenerate all embeddings from scratch
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, with DOI links)
search_fulltext	Search inside PDF content — find concepts, quotes, methods
search_library	Combined metadata + PDF search in one call
search_semantic	Search by meaning using AI embeddings (requires endnote-mcp[semantic])
get_reference_details	Full metadata for a reference (abstract, keywords, DOI, etc.)
get_citation	Format as APA 7th, Harvard, Vancouver, Chicago, or IEEE
get_bibtex	Export references as BibTeX entries for LaTeX
get_bibliography	Generate a formatted bibliography for multiple references
find_related	Find similar references (uses embeddings when available)
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:

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

Operation	Time (4,000 references)
Metadata indexing	~1 second
PDF extraction (first time)	~1 min per 100 PDFs
PDF extraction (incremental)	Only new PDFs
Embedding generation	~3 minutes
Keyword search	< 50 ms
Semantic search	< 200 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
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

Client reports the server "failed to connect" / CONNECTION_CLOSED — The client hides the underlying error. Run echo '' | endnote-mcp serve to see the real traceback (the JSON decode error it prints afterwards is just the empty input, not a fault).

Releasing

Publishing runs on a tag push via .github/workflows/release.yml, which uploads to PyPI and the MCP Registry using OIDC — no API tokens are stored in the repository.

The version lives in seven places, and the registry rejects a server.json that does not exactly match the published PyPI release. Bump all of them, then verify before tagging:

# pyproject.toml, server.json (x2), CITATION.cff, the README citation
# block, mcpb/manifest.json and mcpb/pyproject.toml
python scripts/check_version.py v1.4.12

git commit -am "Bump version to 1.4.12"
git tag v1.4.12 && git push origin main --tags

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 1.4.12) [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.