# omophub-mcp

Connects AI agents to OHDSI medical vocabularies. It enables clinical term lookup and cross-mapping between ICD-10, SNOMED, and RxNorm without local SQL databases.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 5
- Author: OMOPHub
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/OMOPHub/omophub-mcp
- Updated: 2026-10-21
- HTML: https://affpapa.org/en/nevibecode/mcp/omophub-mcp

## What it does

The server links coding assistants with the ATHENA repository directly through protocol tools. Instead of downloading heavy archive dumps and managing relational tables, the model queries endpoints using `search_concepts`, `get_hierarchy`, and `map_concept`. Phenotype cohort assembly becomes straightforward.

Under the hood, the package supports semantic similarity lookups, code verification, and taxonomy exploration across more than 120 systems. You need an `OMOPHUB_API_KEY` token configured in the environment. Without an active secret key, outgoing vocabulary queries fail immediately. Clients can run the process via `npx` or talk to a shared HTTP endpoint.

## Requirements
- Needs: Node.js (commands run via npx)
- Environment variables: `OMOPHUB_API_KEY` — keys and tokens: ask the human for the values, never commit them or put them in shared files.

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add omophub-mcp -e OMOPHUB_API_KEY=<OMOPHUB_API_KEY> -- npx -y @omophub/omophub-mcp
```
Replace <…> with your own values

### Codex

**Platform CLI**
```bash
codex mcp add omophub-mcp --env OMOPHUB_API_KEY=<OMOPHUB_API_KEY> -- npx -y @omophub/omophub-mcp
```
Replace <…> with your own values

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "omophub-mcp": {
            "command": "npx",
            "args": [
                "-y",
                "@omophub/omophub-mcp"
            ],
            "env": {
                "OMOPHUB_API_KEY": "<OMOPHUB_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "omophub-mcp": {
            "type": "stdio",
            "command": "npx",
            "args": [
                "-y",
                "@omophub/omophub-mcp"
            ],
            "env": {
                "OMOPHUB_API_KEY": "<OMOPHUB_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add -e OMOPHUB_API_KEY=<OMOPHUB_API_KEY> omophub-mcp npx -y @omophub/omophub-mcp
```
Replace <…> with your own values

## When to use it
- locate standard concept IDs for clinical diagnoses
- map classification terms from ICD-10 into SNOMED
- trace ancestral hierarchies for phenotype cohort definitions
- validate medical terminology against reference standard vocabularies

## Example prompts
- Find the standard concept reference for chronic obstructive pulmonary disease.
- Convert the billing code E11.9 into its matching SNOMED representation.
- List the direct descendants of coronary artery disease in the hierarchy.

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