Biomedical Python Packages

scispacy

A full spaCy pipeline and models for scientific/biomedical documents.

biocypher

A unifying framework for biomedical research knowledge graphs

pyradigm

Research data management in biomedical and machine learning applications

bent

Biomedical Term Annotator

bio-epidemiology-ner

Recognize bio-medical entities from a text corpus

fedbiomed

A collaborative learning framework for empowering biomedical research

medpalm

MedPalm - Pytorch

optimuskg

Client library for loading the OptimusKG biomedical knowledge graph from Harvard Dataverse.

pybiodatafuse

Python package for biodatafuse project.

zensols-mimicsid

MIMIC-III corpus parsing and section prediction with MedSecId (COLING paper)

farabio

:robot: PyTorch toolkit for biomedical imaging :heart:

skill-to-mcp

Convert AI Skills (Claude Skills format) to MCP server resources - Part of BioContextAI

refsig

Package for obtaining the referential signal from a set of iEEG data

pywinding

A tool for rapidly prototyping wound induction microcoils using Finite Element Method Magnetics (FEMM).

node-synonymizer

SRI Node Normalizer / Name Resolver client for CURIE and name lookup in Translator applications.

zensols-clinicamr

Clincial Domain Abstract Meaning Representation Graphs

zensols-dsprov

Provenience of discharge summaries Pythonic access (BioNLP paper)