OMOPHub MCP Server for Claude, Cursor, and VS Code

What is the MCP Server?

The OMOPHub MCP Server connects your AI assistant to the entire OHDSI ATHENA vocabulary. No database setup, no CSV wrangling - just ask your AI about medical concepts and get verified answers.

You: "Map ICD-10 code E11.9 to SNOMED"

Claude: Found it - E11.9 (Type 2 diabetes mellitus without complications)
        maps to SNOMED concept 201826 (Type 2 diabetes mellitus)
        via standard 'Maps to' relationship.

Hosted MCP - No Installation Required

Skip installation entirely. Connect your AI client directly to mcp.omophub.com with just your API key.

Installation

Install via npm - no build step required:

npm install -g @omophub/omophub-mcp

Or run directly with npx:

npx -y @omophub/omophub-mcp

Claude Desktop

Open Claude Desktop settings > Developer tab > Edit Config. Add to claude_desktop_config.json:

{
  "mcpServers": {
    "omophub": {
      "command": "npx",
      "args": ["-y", "@omophub/omophub-mcp"],
      "env": {
        "OMOPHUB_API_KEY": "oh_your_key_here"
      }
    }
  }
}

Claude Code

claude mcp add omophub -- npx -y @omophub/omophub-mcp
# Then set OMOPHUB_API_KEY in your environment

Cursor

Open the command palette > Cursor Settings > MCP > Add new global MCP server. Add to .cursor/mcp.json:

{
  "mcpServers": {
    "omophub": {
      "command": "npx",
      "args": ["-y", "@omophub/omophub-mcp"],
      "env": {
        "OMOPHUB_API_KEY": "oh_your_key_here"
      }
    }
  }
}

VS Code

Add to .vscode/mcp.json:

{
  "servers": {
    "omophub": {
      "command": "npx",
      "args": ["-y", "@omophub/omophub-mcp"],
      "env": {
        "OMOPHUB_API_KEY": "oh_your_key_here"
      }
    }
  }
}

Windsurf

Add to your Windsurf MCP configuration:

{
  "mcpServers": {
    "omophub": {
      "command": "npx",
      "args": ["-y", "@omophub/omophub-mcp"],
      "env": {
        "OMOPHUB_API_KEY": "oh_your_key_here"
      }
    }
  }
}

Available Tools

Tool	Description
`search_concepts`	Search for medical concepts by name or clinical term across all vocabularies
`get_concept`	Get detailed info about a specific OMOP concept by `concept_id`
`get_concept_by_code`	Look up a concept using a vocabulary-specific code (e.g., ICD-10 `E11.9`)
`map_concept`	Map a concept to equivalent concepts in other vocabularies
`get_hierarchy`	Navigate concept hierarchy - ancestors, descendants, or both
`list_vocabularies`	List available medical vocabularies with statistics
`semantic_search`	Search using natural language with neural embeddings - understands clinical meaning
`find_similar_concepts`	Find concepts similar to a reference concept, name, or description
`explore_concept`	Get concept details, hierarchy, and cross-vocabulary mappings in one call

Tools Reference

See detailed parameter schemas and examples for each tool.

Environment Variables

Variable	Required	Description
`OMOPHUB_API_KEY`	Yes	Your OMOPHub API key
`OMOPHUB_BASE_URL`		Custom API base URL (default: `https://api.omophub.com/v1`)
`OMOPHUB_LOG_LEVEL`		`debug` · `info` · `warn` · `error` (default: `info`)
`OMOPHUB_ANALYTICS_OPTOUT`		Set to `true` to disable analytics headers
`MCP_TRANSPORT`		`stdio` (default) or `http`
`MCP_PORT`		HTTP server port (default: `3100`, only with `http` transport)
`HEALTH_PORT`		Port for standalone health endpoint in stdio mode

Example Prompts

Try these after installing:

“What’s the OMOP concept ID for type 2 diabetes?”

“Map ICD-10 code E11.9 to SNOMED”

“Show me all descendants of Diabetes mellitus in SNOMED”

“Search for metformin in RxNorm”

“Help me build a concept set for heart failure including all descendants”

“Find concepts related to ‘heart attack’” (uses semantic search)

“Give me everything about SNOMED concept 201826” (uses explore)

“What concepts are similar to ‘Type 2 diabetes mellitus’?”

Troubleshooting

Error	Solution
`API key required`	Set `OMOPHUB_API_KEY` in your environment or MCP config
`Authentication failed`	API key may be invalid or expired - generate a new one
`Rate limit exceeded`	Automatic retries are built in. For higher limits, upgrade your plan
Tools not appearing	Restart your AI client, verify `npx @omophub/omophub-mcp` runs without errors

Get Started

MCP Server

Docs for Agents

Integration

OMOPHub MCP Server for Claude, Cursor, and VS Code

What is the MCP Server?

Hosted MCP - No Installation Required

Installation

Claude Desktop

Claude Code

Cursor

VS Code

Windsurf

Available Tools

Tools Reference

Environment Variables

Example Prompts

Troubleshooting

​What is the MCP Server?

Hosted MCP - No Installation Required

​Installation

​Claude Desktop

​Claude Code

​Cursor

​VS Code

​Windsurf

​Available Tools

Tools Reference

​Environment Variables

​Example Prompts

​Troubleshooting

What is the MCP Server?

Installation

Claude Desktop

Claude Code

Cursor

VS Code

Windsurf

Available Tools

Environment Variables

Example Prompts

Troubleshooting