Is Omop_mcp safe to use?

Omop_mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.

How do I install Omop_mcp?

Omop_mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.

What can Omop_mcp do?

Omop_mcp provides 3 tools: find_omop_concept, map_clinical_terminology, batch_concept_mapping. See the full tools list on the server page for descriptions and parameters.

What AI clients work with Omop_mcp?

Omop_mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.

Is Omop_mcp actively maintained?

Omop_mcp is actively maintained — last commit was 19 days ago. It has 35 GitHub stars.

Omop_mcp

Name: Omop_mcp
Author: OHNLP

by OHNLP

Model Context Protocol (MCP) server for mapping clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models

35 3 tools GitHub

No known CVEs

No license

Actively maintained

Last commit 19d ago

Works with most clients

Transport: stdio

3 tools

Grade F

Edit this pageView history

Health

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "omop-mcp": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/omop-mcp)](https://mcppedia.org/s/omop-mcp)

Read me

What Omop_mcp does

Model Context Protocol (MCP) server for mapping clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models (LLMs). The vocabulary API is supported by OMOP HUB, and you can obtain an API key from omophub.com.

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

35/100across 5 weighted dimensions

How we score →

0255075100

−65

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (3)

Click any tool to inspect its schema.

Inventory

Resources (2)

omop_cdm_documentation

Live OMOP Common Data Model documentation

https://omophub.com

omop_concept

OMOP concept details and information

https://omophub.com/concepts/{concept_id}

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Omop_mcp safe to use?: Omop_mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install Omop_mcp?: Omop_mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.
What can Omop_mcp do?: Omop_mcp provides 3 tools: find_omop_concept, map_clinical_terminology, batch_concept_mapping. See the full tools list on the server page for descriptions and parameters.
What AI clients work with Omop_mcp?: Omop_mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.
Is Omop_mcp actively maintained?: Omop_mcp is actively maintained — last commit was 19 days ago. It has 35 GitHub stars.

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Community

Discussion

Start a conversation

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Has anyone used this with Cursor?How do you handle auth?Any alternatives?

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Health

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "omop-mcp": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/omop-mcp)](https://mcppedia.org/s/omop-mcp)

Read me

What Omop_mcp does

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

README

OMOP MCP Server

Model Context Protocol (MCP) server for mapping clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models (LLMs). The vocabulary API is supported by OMOP HUB, and you can obtain an API key from omophub.com.

Demo Website

Overview

This server provides an agentic framework to standardize medical terms into the OMOP Common Data Model (CDM). It uses the OMOPHub API for vocabulary searching, concept suggestion, and terminology mapping.

Installation

Before configuring the MCP server, ensure you have:

uv installed on your system
- Install from: https://docs.astral.sh/uv/getting-started/installation/

Clone the repository

git clone https://github.com/OHNLP/omop_mcp.git
cd omop_mcp

Set up environment variables

Copy .env.template to .env and fill in your API credentials. You will need both an LLM provider key and an OMOPHUB_API_KEY (for vocabulary lookups).
```
cp .env.template .env
```

Configuration for Claude Desktop

Add the following configuration to your claude_desktop_config.json file:

Location:

MacOS: ~/Library/Application\ Support/Claude/claude_desktop_config.json
Windows: %APPDATA%/Claude/claude_desktop_config.json

Configuration:

Replace <path-to-local-repo> with the actual path to your cloned repository.

{
  "mcpServers": {
    "omop_mcp": {
      "command": "uv",
      "args": ["--directory", "<path-to-local-repo>", "run", "omop_mcp"]
    }
  }
}

Features

The OMOP MCP server provides tools and resources for:

Mapping clinical terminology: Intelligent mapping of free-text terms to standardized OMOP concepts.
Vocabulary Search: Direct access to OMOP vocabulary via find_omop_concept.
Batch Processing: Tool for mapping multiple concepts from a CSV file.
Preferred Vocabularies: Automatic domain-specific vocabulary prioritization (e.g., LOINC for measurements, SNOMED for conditions).
Live Documentation: Resource access to live OMOP CDM documentation.

Usage Example

The agent is most effective when you provide context such as the OMOP table or field name.

Prompt:

Map `Temperature Temporal Scanner - RR` for `measurement_concept_id` in the `measurement` table.

Response Example:

CONCEPT_ID: 46235152
CODE: 75539-7
NAME: Body temperature - Temporal artery
CLASS: Clinical Observation
CONCEPT: Standard
VALIDITY: Valid
DOMAIN: Measurement
VOCAB: LOINC
REASON: This LOINC concept specifically represents body temperature measured at the temporal artery.
URL: https://omophub.com/concepts/46235152

Contributing

See CONTRIBUTING.md for guidelines to contribute to the project.

Citation Policy

If you use this software, please cite the pre-print at arXiv (cs.AI) below:

An Agentic Model Context Protocol Framework for Medical Concept Standardization

License

This project is licensed under the Apache License 2.0. See LICENSE file for details.

Contact: jaerongahn@gmail.com

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

35/100across 5 weighted dimensions

How we score →

0255075100

−65

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (3)

Click any tool to inspect its schema.

Inventory

Resources (2)

omop_cdm_documentation

Live OMOP Common Data Model documentation

https://omophub.com

omop_concept

OMOP concept details and information

https://omophub.com/concepts/{concept_id}

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Omop_mcp safe to use?: Omop_mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install Omop_mcp?: Omop_mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.
What can Omop_mcp do?: Omop_mcp provides 3 tools: find_omop_concept, map_clinical_terminology, batch_concept_mapping. See the full tools list on the server page for descriptions and parameters.
What AI clients work with Omop_mcp?: Omop_mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.
Is Omop_mcp actively maintained?: Omop_mcp is actively maintained — last commit was 19 days ago. It has 35 GitHub stars.