omophub-mcp — Claude Code MCP server: what it does, how to install
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.
claude mcp add omophub-mcp -e OMOPHUB_API_KEY=<OMOPHUB_API_KEY> -- npx -y @omophub/omophub-mcpWhat omophub-mcp 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.
What it helps with
- 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 for the agent
- 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.
How to install omophub-mcp
Platform CLI
claude mcp add omophub-mcp -e OMOPHUB_API_KEY=<OMOPHUB_API_KEY> -- npx -y @omophub/omophub-mcpReplace <…> with your own values
Platform CLI
codex mcp add omophub-mcp --env OMOPHUB_API_KEY=<OMOPHUB_API_KEY> -- npx -y @omophub/omophub-mcpReplace <…> with your own values
Config file
{
"mcpServers": {
"omophub-mcp": {
"command": "npx",
"args": [
"-y",
"@omophub/omophub-mcp"
],
"env": {
"OMOPHUB_API_KEY": "<OMOPHUB_API_KEY>"
}
}
}
}Replace <…> with your own values
Config file
{
"servers": {
"omophub-mcp": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"@omophub/omophub-mcp"
],
"env": {
"OMOPHUB_API_KEY": "<OMOPHUB_API_KEY>"
}
}
}
}Replace <…> with your own values
Platform CLI
gemini mcp add -e OMOPHUB_API_KEY=<OMOPHUB_API_KEY> omophub-mcp npx -y @omophub/omophub-mcpReplace <…> with your own values
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about omophub-mcp
How do I install omophub-mcp in Claude Code?
Run claude mcp add omophub-mcp -e OMOPHUB_API_KEY=<OMOPHUB_API_KEY> -- npx -y @omophub/omophub-mcp. Replace the placeholder with your actual access key from your account dashboard.
What is omophub-mcp used for?
It provides MCP tools for searching, navigating, and mapping clinical vocabularies like LOINC, RxNorm, and SNOMED. Agents can inspect medical codes without maintaining local vocabulary databases.
Is an API key required to run the server?
Yes, requests require a valid OMOPHUB_API_KEY environment variable. You generate this credential in the OMOPHub dashboard prior to running the client command.
