MeSH MCP

An experimental MCP (Model Context Protocol) server connecting Claude to the U.S. National Library of Medicine (NLM) Medical Subject Headings (MeSH) linked data APIs, built to investigate the potential of large language models in subject analysis and authority control.

What This Server Does

MeSH MCP connects Claude Desktop to the NLM MeSH APIs, allowing you to search and retrieve MeSH authority data directly within your AI-assisted cataloging workflow.

Once installed, you can ask Claude things like:

"Search MeSH for terms related to osmotic stress"
"Find the MeSH descriptor for CRISPR gene editing"
"What is the scope note for this MeSH descriptor?"
"Look up the full record for descriptor D011506"

The server handles all the API calls, parses the responses, and returns structured data Claude can reason about.

Who This Is For

Catalogers and metadata staff using Claude Desktop who want AI-assisted subject description grounded in real MeSH vocabulary data
Library and repository staff working with health sciences or biomedical research outputs — theses, datasets, grey literature — where MeSH is the preferred controlled vocabulary
Developers integrating MeSH lookups into MCP-based systems

Tools

| Tool | Description | |------|-------------| | search_mesh | Search MeSH descriptors by label using the NLM lookup autocomplete endpoint. Supports startsWith (default), contains, and exact matching. Returns a list of {label, ui, uri} dicts. | | get_mesh_record | Retrieve the full record for a MeSH descriptor by UI code or URI. Returns label, annotation (scope note), tree numbers, tree categories, broader descriptors, see-also cross-references, and qualifier count. | | get_mesh_qualifiers | Retrieve the allowable subheading qualifiers for a descriptor (e.g. Diabetes Mellitus/therapy). Optionally includes per-qualifier indexing annotations. | | get_mesh_tree | Retrieve the MeSH tree hierarchy for a descriptor: tree numbers, top-level category names, and immediate broader (parent) descriptors. |

Notes on Search Behaviour

search_mesh uses left-anchored matching by default (startsWith), which matches from the beginning of the heading label. Searching diabetes will find Diabetes Mellitus and related headings, but searching mellitus will not. When a startsWith search returns no results, use match="contains" to search anywhere in the label.

For highly specialized or emerging concepts without a direct MeSH equivalent — such as specific protein families or recently coined terminology — search with a broader parent term and review the returned hierarchy to identify the best available descriptor.

Use get_mesh_record to verify before assigning. Retrieve the full record to confirm the scope note matches the intended concept, particularly when multiple candidate terms are returned. Tree numbers indicate where the term sits in the MeSH hierarchy and can guide selection of broader or narrower terms.

Installation

Requirements

Python 3.11 or later
Claude Desktop (or another MCP-compatible host)

Install from GitHub

pip install git+https://github.com/YOUR_USERNAME/mesh-mcp.git

Install from a local clone

git clone https://github.com/YOUR_USERNAME/mesh-mcp.git
cd mesh-mcp
pip install -e .

On Windows with Anaconda, use Anaconda Prompt and add --break-system-packages if prompted.

Claude Desktop Configuration

After installation, add the server to your claude_desktop_config.json. Claude Desktop uses a restricted PATH that does not include the Python bin directory, so the full path to the command is required.

To find your exact path, run the following in Terminal (Mac) or Anaconda Prompt (Windows):

Mac: which mesh-mcp
Windows: where mesh-mcp

The examples below are illustrative only — your actual path will differ depending on your Python version and installation method.

Mac (example):

{
  "mcpServers": {
    "mesh": {
      "command": "/Library/Frameworks/Python.framework/Versions/3.13/bin/mesh-mcp"
    }
  }
}

Windows/Anaconda (example):

{
  "mcpServers": {
    "mesh": {
      "command": "C:\\Users\\username\\anaconda3\\Scripts\\mesh-mcp.exe"
    }
  }
}

Always replace the path with the actual output of the which or where command on your machine.

Finding your config file:

Mac: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: %APPDATA%\Claude\claude_desktop_config.json

After editing the config, quit Claude Desktop completely and reopen it. The MeSH tools will be available in your next conversation.

Verifying the installation

Once Claude Desktop is open, ask: "What cataloger tools do you have available?" — you should see all four MeSH tools listed.

Troubleshooting

Tools not appearing in Claude Desktop

Confirm the package installed without errors: pip show mesh-mcp
Confirm the command is available: mesh-mcp --help (should start the server, not throw an error)
Check that the config file path is correct for your OS
Quit Claude Desktop fully (not just close the window) before reopening

Changes to server.py not taking effect

Python caches compiled bytecode in __pycache__ folders. After editing server.py, delete any __pycache__ folders in the package directory and restart Claude Desktop fully.

Data Source

MeSH is produced by the U.S. National Library of Medicine and is freely available with no license required. Attribution is appreciated.

License

GPLv3. See LICENSE.

Development Note

The code in this project was developed in collaboration with Claude, Anthropic's AI assistant. The design decisions — including tool selection, search protocols, and the application of MeSH cataloging practice to the server's behaviour — reflect the author's professional cataloging expertise. Claude handled the implementation of those decisions in Python.

Acknowledgement

This project was inspired by and adapted from KL Tang's cataloger-mcp, extended here to apply to MeSH vocabulary lookup.

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