Ehr Python Packages

mirobody

Turn scattered health data into answers you can trace. Self-hosted AI health data engine for lab reports, wearables and genetics, with a built-in MCP server. Run it with Docker and one LLM key, or keep every model local on llama.cpp.

meds-reader

A high-performance database and Python reader interface for MEDS datasets

medpython

Medial Research Libs Infrastructure

ehrdata

A datastructure for EHR data

faker-healthcare-provider

🏥 Faker provider for generating healthcare fake data - diseases, ICD-10, drugs, procedures

ehrapy

Electronic Health Record Analysis with Python.

clinosim

Clinically Realistic Hospital Data Simulator — FHIR R4 synthetic EHR data with physiological coherence. Built at InterSystems.

healthchain

Python SDK for healthcare AI — typed, validated FHIR tools for agents, real-time EHR connectivity, production deployment ✨ 🏥

sekmet-fhir

Micro hospital information system (HIS) for testing HIS/EHR/LIS FHIR R4 integrations end to end: ADT, orders & results, scheduling, pharmacy, billing workflows; lab/RIS/payer simulator; Subscriptions, Bulk Data, SMART, TestScript and load testing.

ehr2rl

Convert MIMIC-IV EHR data into offline reinforcement learning datasets for healthcare research.

cycquery

A tool to query relational EHR databases

fhirpack

FHIR Python Analysis Client and Kit (FHIRPACK) is a general purpose FHIR client that simplifies the access, analysis and representation of FHIR and EHR data using PANDAS, an ETL philosophy and a functional syntax. It was initially developed at the IKIM and HDDBS in Germany. Read more at https://zenodo.org/record/8006589

pat2vec

A comprehensive Python package for healthcare data engineering, designed to extract, transform, and feature engineer patient data from CogStack-based EHR datalakes. Enables patient-level aggregation, longitudinal time series construction (up to 25 years retrospective), flexiblefeature engineering (biochemistry, demographics, medications, diagnoses

medpython-etl

Medial Research Tools for Machine learning in medical data, EMR

cleandat

Python functions to facilitate the pre-processing of data for ML tasks in a clinical context

yaib

🧪Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109

ehrax

io+hdf5+lazy-loading+processing-pipelines for EHRs and generic PyTrees for JAX friendly tasks, mainly ML

chartfold

Patient-facing tool for consolidating personal health data from multiple EHR systems into a single SQLite database

lemonpie

A deep learning library for Electronic Health Record (EHR) data

oneehr

[KDD 2026] An all-in-one EHR predictive modeling and analysis library in Python

hebrah

Official Python SDK for the Hebrah healthcare connectivity platform — FHIR, HL7 v2, sandbox provisioning, and webhook delivery

openemr-agent

The most popular open source electronic health records and medical practice management solution.

mai-dx

An open source implementation of the paper: "Sequential Diagnosis with Language Models" From Microsoft Built with Swarms Framework