Omophub MCP Server
Search, map, and navigate 10M+ OMOP medical vocabulary concepts with AI.
Data last scanned today · Reviewed today
Overview
OMOPHub MCP Server provides direct access to the OHDSI ATHENA vocabulary through any MCP-compatible client. By removing the need for local database management or large file processing, it allows AI models to perform concept lookups, cross-vocabulary mapping, and hierarchy navigation for standards like SNOMED CT, ICD-10, RxNorm, and LOINC. The tool is designed to assist with phenotype definitions, code validation, and cohort building. Users can query medical vocabularies through natural language prompts, simplifying workflows that otherwise require complex SQL queries or multi-gigabyte data wrangling.
Our verdict
With a security score of 51/100, this server is currently classified as high risk. A major concern is the lack of a read-only mode, as every installation currently operates with full write access. While it is maintained by the official vendor and uses a small dependency footprint, the combination of high-risk permissions and a low bus factor necessitates caution. It is suitable for research and experimentation in isolated environments, but users should carefully audit its usage in sensitive medical workflows.
- Maintained by the official OMOPHub organization
- Uses only two direct dependencies
- Reduces multi-gigabyte data processing for clinical concepts
- Provides immediate access to standard medical vocabularies
- Operates without a read-only mode
- Limited contributor base presents bus-factor risk
- Not yet undergone editorial security review
Setup
{
"mcpServers": {
"omophub-mcp": {
"args": [
"-y",
"@omophub/omophub-mcp"
],
"command": "npx"
}
}
}Paste into ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows), then restart Claude Desktop. Some servers require API keys or tokens as environment variables — check the project's README and add an "env" object if needed.
- No read-only mode — running this grants full read/write access.
Tools
| Tool | Description | Risk |
|---|---|---|
| search_concepts | Search for medical concepts by name or clinical term across all vocabularies | low |
| get_concept | Get detailed info about a specific OMOP concept by concept_id | low |
| get_concept_by_code | Look up a concept using a vocabulary-specific code (e.g., ICD-10 E11.9) | low |
| map_concept | Map a concept to equivalent concepts in other vocabularies | low |
| get_hierarchy | Navigate concept hierarchy - ancestors, descendants, or both | low |
| list_vocabularies | List available medical vocabularies with statistics | low |
| semantic_search | Search using natural language with neural embeddings (understands clinical meaning) | low |
| find_similar_concepts | Find concepts similar to a reference concept, name, or description | low |
| explore_concept | Get concept details, hierarchy, and cross-vocabulary mappings in one call | low |
| fhir_resolve | Resolve a FHIR coded value (incl. administrative codes via the HL7 FHIR-to-OMOP IG ConceptMaps) to its OMOP standard concept and CDM target table | low |
Compatibility
| Client | Local | Docker | Remote | Read-only |
|---|---|---|---|---|
| Claude Desktop | ||||
| Cursor | ||||
| VS Code | ||||
| Windsurf | ||||
| ChatGPT |
Frequently asked questions
›What is required to use the OMOPHub MCP server?
You must have an active API key, which can be generated by signing up at omophub.com and visiting your dashboard.
›Does the Claude Desktop app support all connection methods for this server?
No, the Claude Desktop Custom Connectors UI does not support custom headers, so you must use the npx setup method for Claude Desktop.
›Can I run the server as a standalone HTTP service?
Yes, you can run the server in HTTP mode using npx or Docker, which allows multiple AI agents to connect to a single instance via a URL.
›Which medical vocabularies are supported?
The server provides access to the OHDSI ATHENA vocabulary, including SNOMED CT, ICD-10, RxNorm, LOINC, and over 100 others.
›How do I provide my API key when using the hosted MCP server?
You must provide your API key via the Authorization header as a Bearer token when connecting your MCP client to mcp.omophub.com.
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