How to add OMOP MCP Server to Claude Desktop

Map clinical terminology to standardized OMOP CDM concepts using LLMs and the OMOPHub vocabulary API. Paste the config into ~/Library/Application Support/Claude/claude_desktop_config.json and restart Claude Desktop.

Last updated June 14, 2026 · 36★ · stdio · apikey

Claude Desktop config for OMOP MCP Server

git clone https://github.com/OHNLP/omop_mcp.git

{
  "mcpServers": {
    "omop-mcp-server": {
      "command": "uv",
      "args": [
        "--directory",
        "<path-to-local-repo>",
        "run",
        "omop_mcp"
      ]
    }
  }
}

Setup steps

1Open Claude Desktop → Settings → Developer → Edit Config (this opens ~/Library/Application Support/Claude/claude_desktop_config.json).
2Paste the OMOP MCP Server config below under the top-level "mcpServers" key.
3Fill in any placeholder secrets (API keys, paths) in the snippet.
4Save the file, then fully quit and reopen Claude Desktop.
5Open a chat and confirm OMOP MCP Server's tools appear under the 🔌 tools menu.

Before you start

uv installed (https://docs.astral.sh/uv/getting-started/installation/)
Clone of the OHNLP/omop_mcp repository
OMOPHUB_API_KEY from omophub.com for vocabulary lookups
An LLM provider API key (e.g. OpenAI, Anthropic, Azure OpenAI, OpenRouter, Groq, Hugging Face, or Google), configured via a local .env file

What OMOP MCP Server can do in Claude Desktop

find_omop_concept

Search the OMOP vocabulary directly to look up standardized concepts.

map_clinical_terminology

Intelligently map a free-text clinical term to a standardized OMOP concept, optionally guided by the target OMOP table/field, returning the concept id, code, name, class, validity, domain, vocabulary, and a rationale.

batch_mapping

Map multiple clinical concepts at once from a CSV file.

Security

Requires an OMOPHUB_API_KEY (from omophub.com) and at least one LLM provider key (OpenAI, Anthropic, Azure OpenAI, OpenRouter, Groq, Hugging Face, or Google). Credentials are supplied via a local .env file copied from .env.template; do not commit the .env file. Clinical terms you map are sent to the configured LLM provider and the OMOPHub API.

OMOP MCP Server + Claude Desktop FAQ

Where is the Claude Desktop config file?

Claude Desktop reads MCP servers from ~/Library/Application Support/Claude/claude_desktop_config.json. Paste the OMOP MCP Server config there under the "mcpServers" key and restart the client.

Is OMOP MCP Server safe to use with Claude Desktop?

What vocabulary backend does it use?

It uses the OMOPHub API (omophub.com) for vocabulary search, concept suggestion, and terminology mapping. You need an OMOPHUB_API_KEY.

Which LLM providers are supported?

The .env template includes keys for OpenAI, Anthropic, Azure OpenAI, OpenRouter, Groq, Hugging Face, and Google; fill in only the provider(s) you intend to use.

How do I run it in Claude Desktop?

Clone the repo, install uv, copy .env.template to .env and fill in your keys, then add the provided mcpServers block to claude_desktop_config.json with the path to your local repo.

View repo Full OMOP MCP Server page