OMOP MCP Server

MCP server from the OHNLP clinical-NLP consortium mapping free-text clinical terminology to OMOP Common Data Model concepts using LLMs.

Unsigned

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: 0.2.0
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

Safety classification

No safety classification has been submitted for this entry.

Server manifest

Server name: io.github.ohnlp/omop_mcp
Server version: 0.2.0
Implements: other

Install

{
  "mcpServers": {
    "io.github.ohnlp/omop_mcp": {
      "command": "uv",
      "args": [
        "OHNLP/omop_mcp@0.2.0"
      ]
    }
  }
}

{
  "mcpServers": {
    "io.github.ohnlp/omop_mcp": {
      "command": "uv",
      "args": [
        "OHNLP/omop_mcp@0.2.0"
      ]
    }
  }
}

{
  "mcpServers": {
    "io.github.ohnlp/omop_mcp": {
      "command": "uv",
      "args": [
        "OHNLP/omop_mcp@0.2.0"
      ]
    }
  }
}

Open in Cursor

{
  "servers": {
    "io.github.ohnlp/omop_mcp": {
      "command": "uv",
      "args": [
        "OHNLP/omop_mcp@0.2.0"
      ]
    }
  }
}

{
  "mcpServers": {
    "io.github.ohnlp/omop_mcp": {
      "command": "uv",
      "args": [
        "OHNLP/omop_mcp@0.2.0"
      ]
    }
  }
}

{
  "mcpServers": {
    "io.github.ohnlp/omop_mcp": {
      "command": "uv",
      "args": [
        "OHNLP/omop_mcp@0.2.0"
      ]
    }
  }
}

{
  "mcp": {
    "io.github.ohnlp/omop_mcp": {
      "type": "local",
      "command": [
        "uv",
        "OHNLP/omop_mcp@0.2.0"
      ],
      "enabled": true
    }
  }
}

Provenance

Created: 2026-09-08T00:00:00.000Z
Updated: 2026-09-08T00:00:00.000Z
Last verified: 2026-09-08T00:00:00.000Z