OMOPHub MCP Server

Why OMOPHub MCP?

Working with medical vocabularies today means downloading multi-gigabyte CSV files, loading them into a local database, and writing SQL to find what you need. Every time.

OMOPHub MCP Server gives your AI assistant instant access to the entire OHDSI ATHENA vocabulary. No database setup, no CSV wrangling, no context switching. Just ask.

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.

Use cases:

• Concept lookup - Find OMOP concept IDs for clinical terms in seconds

• Cross-vocabulary mapping - Map between ICD-10, SNOMED, RxNorm, LOINC, and 100+ vocabularies

• Hierarchy navigation - Explore ancestors and descendants for phenotype definitions

• Concept set building - Let your AI agent assemble complete concept sets for cohort definitions

• Code validation - Verify medical codes and check their standard mappings

Quick Start

1. Get an API Key

Sign up at omophub.com → create an API key in your dashboard.

2. Add to Your AI Client

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

Open the command palette and choose "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"
      }
    }
  }
}

Add to .vscode/mcp.json:

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

Run the MCP server as an HTTP service that clients connect to via URL:

# Start HTTP server on port 3100
npx -y @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key_here

# MCP endpoint: http://localhost:3100/mcp
# Health check:  http://localhost:3100/health

Connect MCP clients to / or /mcp. Useful for centralized deployments where multiple AI agents share one server instance.

Connect directly to the OMOPHub-hosted MCP server - no installation required. Each client authenticates with their own API key via the Authorization header:

Claude Code:

claude mcp add omophub --transport http \
  -H "Authorization: Bearer oh_your_key_here" \
  https://mcp.omophub.com

VS Code (.vscode/mcp.json):

{
  "servers": {
    "omophub": {
      "type": "http",
      "url": "https://mcp.omophub.com",
      "headers": { "Authorization": "Bearer oh_your_key_here" }
    }
  }
}

Cursor / Windsurf:

{
  "mcpServers": {
    "omophub": {
      "url": "https://mcp.omophub.com",
      "headers": { "Authorization": "Bearer oh_your_key_here" }
    }
  }
}

Note: Claude Desktop's Custom Connectors UI only supports OAuth and cannot send custom headers. Use the npx setup instead.

# HTTP mode (default in Docker) - serves MCP on port 3100
docker run -e OMOPHUB_API_KEY=oh_your_key_here -p 3100:3100 omophub/omophub-mcp

# Stdio mode (for piping)
docker run -i -e OMOPHUB_API_KEY=oh_your_key_here omophub/omophub-mcp --transport=stdio

3. Start Asking

"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"

Available Tools

Resources

Prompts

Example Prompts

Find a concept → search_concepts

"Search for metformin in RxNorm"

Cross-vocabulary mapping → map_concept

"I have SNOMED concept 201826 - what's the ICD-10 code?"

Build a concept set → search_concepts → get_hierarchy → map_concept

"Help me build a concept set for Type 2 diabetes including all descendants"

Validate a code → get_concept_by_code → map_concept

"Is ICD-10 code E11.9 valid? What does it map to in SNOMED?"

Semantic search → semantic_search

"Find concepts related to 'heart attack'"

Explore a concept → explore_concept

"Give me everything about SNOMED concept 201826"

FHIR-to-OMOP resolution → fhir_resolve

"Resolve FHIR SNOMED code 44054006 to OMOP — what table does it go in?"

CodeableConcept → fhir_resolve_codeable_concept

"This CodeableConcept has both SNOMED 44054006 and ICD-10 E11.9 — which should I use for OMOP?"

Find similar → find_similar_concepts

"What concepts are similar to 'Type 2 diabetes mellitus'?"

Configuration

Environment Variables

CLI Arguments

# Stdio mode (default)
npx @omophub/omophub-mcp --api-key=oh_your_key --base-url=https://custom.api.com/v1

# HTTP mode
npx @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key

# Stdio mode with standalone health endpoint
npx @omophub/omophub-mcp --api-key=oh_your_key --health-port=8080

Health Endpoint (Docker / Kubernetes)

In HTTP mode, the health endpoint is available at /health on the same port as the MCP endpoint:

npx @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key
curl http://localhost:3100/health
# → {"status":"ok","version":"1.5.0","uptime_seconds":42}

In stdio mode, use --health-port for a standalone health endpoint:

HEALTH_PORT=8080 OMOPHUB_API_KEY=oh_your_key npx @omophub/omophub-mcp
curl http://localhost:8080/health

The Docker image defaults to HTTP mode on port 3100 with health checks built in.

Development

git clone https://github.com/OMOPHub/omophub-mcp.git
cd omophub-mcp
npm install
npm run build
npm test

Run locally:

OMOPHUB_API_KEY=oh_your_key npx tsx src/index.ts

Troubleshooting

Links

• Documentation

• Get an API Key

• Python SDK

• Community & Support

License

MIT - see LICENSE