OMOP MCP Server
ohnlp/omop_mcp@1.0.0MCP server from the OHNLP clinical-NLP consortium mapping free-text clinical terminology to OMOP Common Data Model concepts using LLMs.
Overview
A real, currently maintained MCP server (40 GitHub stars, pushed within the month of review) published by OHNLP, an academic clinical natural-language-processing consortium, exposing an LLM-backed find_omop_concept tool that maps free-text clinical terminology to OHDSI's OMOP Common Data Model concepts, the CDM widely used across the OHDSI network to harmonise multi-site EHR and clinical-research data for real-world-evidence studies. The approach is backed by a published paper (arXiv:2509.03828), confirmed from the repository's own README, not merely asserted.
Licensing note: GitHub's own derived licence metadata reports NOASSERTION for this repository (its automatic detector did not recognise the licence text), which is exactly the kind of derived-metadata gap this registry's vetting checklist asks not to trust on its own. Fetched directly, the repository's root LICENSE file is the standard, unmodified Apache License 2.0 text, so Apache-2.0 is recorded here on that direct confirmation, not on GitHub's badge.
Recorded as a marginal fit, plainly: OMOP/OHDSI is not a GA4GH standard, the tool operates on public, standardised vocabularies rather than access-controlled patient data, and it performs terminology mapping, a real, narrowly-scoped, published clinical-NLP task, rather than exposing a genomics or health data source directly. Not published to a package registry (no PyPI package found for omop_mcp); installation is git-clone-and-run via uv.
Details
- Licence
- Apache-2.0
- Version
- 1.0.0
- Category
- Other GA4GH-standard or genomics/health data source
- Homepage
- https://github.com/OHNLP/omop_mcp
- Repository
- https://github.com/OHNLP/omop_mcp
- Maintainers
- Susheel Varma (@susheel, GA4GH AI Workstream / Sage Bionetworks)
- Keywords
- omopohdsiclinical-terminologycommon-data-modelconcept-mappingmcp-server
- GA4GH standards
- other
Publisher
Safety classification
No safety classification has been submitted for this entry.
Server manifest
- Server name
- io.github.ohnlp/omop_mcp
- Server version
- 1.0.0
- Implements
- other
Install
Add this to your Claude Desktop MCP server configuration.
{
"mcpServers": {
"io.github.ohnlp/omop_mcp": {
"command": "uv",
"args": [
"OHNLP/omop_mcp@1.0.0"
]
}
}
}Add this to your Claude Code MCP server configuration.
{
"mcpServers": {
"io.github.ohnlp/omop_mcp": {
"command": "uv",
"args": [
"OHNLP/omop_mcp@1.0.0"
]
}
}
}Add this to your Cursor MCP server configuration.
{
"mcpServers": {
"io.github.ohnlp/omop_mcp": {
"command": "uv",
"args": [
"OHNLP/omop_mcp@1.0.0"
]
}
}
}Add this to your VS Code MCP server configuration.
{
"servers": {
"io.github.ohnlp/omop_mcp": {
"command": "uv",
"args": [
"OHNLP/omop_mcp@1.0.0"
]
}
}
}Add this to your Windsurf MCP server configuration.
{
"mcpServers": {
"io.github.ohnlp/omop_mcp": {
"command": "uv",
"args": [
"OHNLP/omop_mcp@1.0.0"
]
}
}
}Add this to your Kiro MCP server configuration.
{
"mcpServers": {
"io.github.ohnlp/omop_mcp": {
"command": "uv",
"args": [
"OHNLP/omop_mcp@1.0.0"
]
}
}
}Add this to your opencode MCP server configuration.
{
"mcp": {
"io.github.ohnlp/omop_mcp": {
"type": "local",
"command": [
"uv",
"OHNLP/omop_mcp@1.0.0"
],
"enabled": true
}
}
}Provenance
- Created
- Updated
- Last verified