Pyomop

Name: Pyomop
Author: dermatologist

skills · by dermatologist

Python package for managing OHDSI clinical data models. Includes support for LLM based plain text queries, MCP server and FHIR import.

64 1.3M/wk 0 tools GitHub npm PyPI

No known CVEs

GPL-3.0 license

Actively maintained

Last commit 10d ago

Works with most clients

Transport: stdio, sse, http

0 tools

Grade F

Edit this pageView history

Health Data

Step 1

Install in your client

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

Supported in Claude Desktopstdio, sse, http · Node 18+

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

{
  "mcpServers": {
    "pyomop": {
      "args": [
        "-y",
        "skills"
      ],
      "command": "npx"
    }
  }
}

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

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What Pyomop does

pyomop is your OMOP Swiss Army Knife 🔧 for working with OHDSI OMOP Common Data Model (CDM) v5.4 or v6 compliant databases using SQLAlchemy as the ORM. It supports converting query results to pandas DataFrames for machine learning pipelines and provides utilities for working with OMOP vocabularies. Table definitions are based on the omop-cdm library. Pyomop is designed to be a lightweight, easy-to-use library for researchers and developers experimenting and testing with OMOP CDM databases. It ca

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Score breakdown

64/100across 5 weighted dimensions

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−36

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Security

OSV.dev

No known CVEs.

Checked skills against OSV.dev.

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Frequently Asked Questions

Is Pyomop safe to use?: Pyomop 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. Licensed under GPL-3.0.
How do I install Pyomop?: Pyomop supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.
What AI clients work with Pyomop?: Pyomop is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.
Is Pyomop actively maintained?: Pyomop is actively maintained — last commit was 10 days ago. It has 64 GitHub stars.

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✨ Overview

pyomop is your OMOP Swiss Army Knife 🔧 for working with OHDSI OMOP Common Data Model (CDM) v5.4 or v6 compliant databases using SQLAlchemy as the ORM. It supports converting query results to pandas DataFrames for machine learning pipelines and provides utilities for working with OMOP vocabularies. Table definitions are based on the omop-cdm library. Pyomop is designed to be a lightweight, easy-to-use library for researchers and developers experimenting and testing with OMOP CDM databases. It can be used both as a commandline tool and as an imported library in your code.

Supports SQLite, PostgreSQL, and MySQL. CDM and Vocab tables are created in the same schema. (See usage below for more details)

LLM-based natural language queries via langchain. Usage.

🔥 FHIR to OMOP conversion utilities. (See usage below for more details)

Execute QueryLibrary. (See usage below for more details)

Please ⭐️ If you find this project useful!

Docker

A docker-compose is provided to quickly set up an environment with postgrs, webapi, atlas and a sql script to create a source in webapi. The script can be run using the psql command line tool or via the webapi UI. Please refresh after running the script by sending a request to /WebAPI/source/refresh.

🔧 Usage

import asyncio import datetime from sqlalchemy import select from pyomop import CdmEngineFactory, CdmVector, CdmVocabulary # cdm6 and cdm54 are supported from pyomop.cdm54 import Base, Cohort, Person, Vocabulary async def main(): cdm = CdmEngineFactory() # Creates SQLite database by default for fast testing # cdm = CdmEngineFactory(db='pgsql', host='', port=5432, # user='', pw='', # name='', schema='') # cdm = CdmEngineFactory(db='mysql', host='', port=3306, # user='', pw='', # name='') engine = cdm.engine # Comment the following line if using an existing database. Both cd ... [View full README on GitHub](https://github.com/dermatologist/pyomop#readme)

Frequently Asked Questions

Is Pyomop safe to use?

Pyomop 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. Licensed under GPL-3.0.

How do I install Pyomop?

Pyomop supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.

What AI clients work with Pyomop?

Pyomop is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.

Is Pyomop actively maintained?

Pyomop is actively maintained — last commit was 10 days ago. It has 64 GitHub stars.