{"repo":"dermatologist/pyomop","free":true,"listed":false,"github":"https://github.com/dermatologist/pyomop","clone":"git clone https://github.com/dermatologist/pyomop.git","description":"Python package for managing OHDSI clinical data models. Includes support for LLM based plain text queries, MCP server and FHIR import.","language":"Python","stars":66,"topics":["ohdsi","datawarehouse","health-informatics","health-data-analysis","clinical-trials","cdm","python","hacktoberfest","llm","text-to-sql"],"license":"GPL-3.0","category":"ai-agents","readme_excerpt":"pyomop: OMOP Swiss Army Knife 🔧 ✨ 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! Installation Stable release: Development version: LLM support: ✨ See this notebook or script for examples. 👇 MCP SERVER is recommended for advanced usage. 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 🔥 FHIR to OMOP mapping pyomop can loa","default_branch":null,"files":null,"tree":[],"storefront":"/r/dermatologist","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/dermatologist/pyomop/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}