Medical Informatics Python Packages

medspacy-quickumls

System for Medical Concept Extraction and Linking

iamsystem

Fast dictionary-based approach for semantic annotation / entity linking

pycohortflow

Lightweight Cohort Flow Diagrams built on Matplotlib — with an interactive browser-based generator.

pat2vec

A comprehensive Python package for healthcare data engineering, designed to extract, transform, and feature engineer patient data from CogStack-based electronic health record (EHR) datalakes. It provides tools for cohort building, batch data processing, clinical note analysis, and creating machine learning-ready datasets.

quickumls

System for Medical Concept Extraction and Linking

contextualized-ml

An SKLearn-style toolbox for estimating and analyzing models, distributions, and functions with context-specific parameters.

fhirpack

FHIRPACK (FHIR Python Analysis Client and Kit) 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.

umls-graph

Build a medical knowledge graph based on Unified Language Medical System (UMLS)

csg-dicoms-anonymizer

Robust and easy to use generic dicoms anonymizer with demographics csv spreadsheet anonymization by hashed ids

openemr-agent

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