Endnote MCP

Name: Endnote MCP
Author: gokmengokhan

by gokmengokhanversion 1.4.15i★ –iRuns on your computer

Registry nameio.github.gokmengokhan/endnote-mcp

Install

Overview

Description from the maker (original English)

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

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi1 of 1 passedChecked from public information; code not scanned yet
UsageiNot measured yet★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs on your computer
Transport: stdio
Category: Search & AI memory

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 1 of 1 passed
Runs on your computer with your user’s permissions (files, network, apps).
The registry lists no key to fill in.

You need

PyPIPython’s uv installed (for the uvx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Open Claude Desktop → Settings → Developer → Edit Config, and paste this into claude_desktop_config.json

{
  "mcpServers": {
    "endnote": {
      "command": "uvx",
      "args": [
        "endnote-mcp"
      ]
    }
  }
}

Run this in your terminal

claude mcp add endnote -- uvx endnote-mcp

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "endnote": {
      "command": "uvx",
      "args": [
        "endnote-mcp"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "endnote": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "endnote-mcp"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

This one runs on your computer, and ChatGPT can only connect to servers on the internet. Pick another app.

Your choice stays on this device in a cookie; no account needed.

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Runs on your computer; the tool list appears in your AI app after you install it.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 8, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account gokmengokhan, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
– Not applicable
Endpoint responds
This one runs on your computer; there is no internet endpoint
– Not applicable
Sign-in with OAuth
Runs on your computer and uses local settings instead
… Not checked yet
No hidden instructions in tool descriptions
Runs on your computer; we can only read tool lists from internet endpoints

Compared with others in Search & AI memoryi

More stars than 0% of the other 5668 servers in this category
Published to the registry more recently than 72% of the other 5668 servers in this category
Basic checks equal to or better than 100% of the other 5668 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is Endnote MCP safe?

It passed 1 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

It runs on your computer. Your AI app starts it when needed, and data does not pass through the maker’s servers (unless it calls an online service itself).

Is it still maintained?

The GitHub repo last changed –, and the latest version (1.4.15) reached the registry 15 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. You also need Python (uv) on your computer.

What can I use instead?

In the same category: Context7, Codebase Memory, Exa

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Reading a card:★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi

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README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

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.

Export your library from EndNote. File → Export → choose XML format → save somewhere like Desktop.
Download endnote-mcp.mcpb from the latest release.
Double-click the `.mcpb` file (or in Claude Desktop: Settings → Extensions → Install Extension…).
In the install dialog, point Claude Desktop at:

Your EndNote XML file (from step 1)
Your PDF Attachments Folder — usually .Data/PDF/ next to your .enl file, or PDF/ inside an .enlp package.

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.

Claude Code Plugin and Agent Skill

The repo includes a skill, endnote-library, that teaches an agent how to work with your library: cite only records the tools return, take page numbers from the printed page rather than the PDF position, check quotations word for word, and verify a draft's references one by one.

Claude Code. Install the CLI and index your library first (steps 1–3 above), then run:

/plugin install endnote --marketplace gokmengokhan/endnote-mcp

On Claude Code before 2.1.275, run /plugin marketplace add gokmengokhan/endnote-mcp, then /plugin install endnote@endnote-mcp. The plugin adds the skill and starts the server with endnote-mcp serve, so that command must be on your PATH. If you already added the server with claude mcp add and the same command, Claude Code connects it only once; if yours uses another command or path, remove it with claude mcp remove endnote to avoid duplicate tools.

Claude Desktop. Zip the plugin/skills/endnote-library/ folder and upload it under Customize > Skills.

Other agents. Agents that read Agent Skills (SKILL.md folders) can use the same skill: copy plugin/skills/endnote-library/ into the agent's skills directory.

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:

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. 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 v

Only the beginning is shown; read the rest in the repo

Endnote MCP

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Search & AI memoryi

Common questions

Alternatives

Context7

Codebase Memory

Exa

README from the maker

EndNote MCP

What It Does

How It Works

Requirements

Install (Desktop Bundle — Recommended)

Building the bundle yourself

→ dist/endnote-mcp.mcpb

Install (CLI / from PyPI)

1. Install

Or with pip

2. Export your library from EndNote

3. Run the setup wizard

4. Restart Claude Desktop

Claude Code Plugin and Agent Skill

Semantic Search (Optional)

Generate embeddings (~3 min for 4,000 references)

Commands

Tools Available to Claude

Adding New References

Performance

Configuration

Notes fields

Citation Styles

BibTeX Export

Troubleshooting

Releasing

block, mcpb/manifest.json and mcpb/pyproject.toml