Medical Informatics Python Packages

medspacy-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.

quickumls

System for Medical Concept Extraction and Linking

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

iamsystem

Fast dictionary-based approach for semantic annotation / entity linking

pycohortflow

Lightweight cohort flow diagrams built on Matplotlib.

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

umls-graph

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

openemr-agent

Healthcare AI agent sidecar for OpenEMR — clinical decision support with drug interaction checking, patient data retrieval, and safety verification

csg-dicoms-anonymizer

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