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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.

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Installation

Install via npm - no build step required: 
npm install -g @omophub/omophub-mcp
Or run directly with npx: 
npx -y @omophub/omophub-mcp

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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"
      }
    }
  }
}

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Claude Code

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

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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"
      }
    }
  }
}

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VS Code

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

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Windsurf

Add to your Windsurf MCP configuration: 
{
  "mcpServers": {
    "omophub": {
      "command": "npx",
      "args": ["-y", "@omophub/omophub-mcp"],
      "env": {
        "OMOPHUB_API_KEY": "oh_your_key_here"
      }
    }
  }
}

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Available Tools

ToolDescription
search_conceptsSearch for medical concepts by name or clinical term across all vocabularies
get_conceptGet detailed info about a specific OMOP concept by concept_id
get_concept_by_codeLook up a concept using a vocabulary-specific code (e.g., ICD-10 E11.9)
map_conceptMap a concept to equivalent concepts in other vocabularies
get_hierarchyNavigate concept hierarchy - ancestors, descendants, or both
list_vocabulariesList available medical vocabularies with statistics
semantic_searchSearch using natural language with neural embeddings - understands clinical meaning
find_similar_conceptsFind concepts similar to a reference concept, name, or description
explore_conceptGet concept details, hierarchy, and cross-vocabulary mappings in one call

Tools Reference

See detailed parameter schemas and examples for each tool.

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Environment Variables

VariableRequiredDescription
OMOPHUB_API_KEYYesYour OMOPHub API key
OMOPHUB_BASE_URLCustom API base URL (default: https://api.omophub.com/v1)
OMOPHUB_LOG_LEVELdebug · info · warn · error (default: info)
OMOPHUB_ANALYTICS_OPTOUTSet to true to disable analytics headers
MCP_TRANSPORTstdio (default) or http
MCP_PORTHTTP server port (default: 3100, only with http transport)
HEALTH_PORTPort for standalone health endpoint in stdio mode

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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’?”

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Troubleshooting

ErrorSolution
API key requiredSet OMOPHUB_API_KEY in your environment or MCP config
Authentication failedAPI key may be invalid or expired - generate a new one
Rate limit exceededAutomatic retries are built in. For higher limits, upgrade your plan
Tools not appearingRestart your AI client, verify npx @omophub/omophub-mcp runs without errors