Biomedical Python Packages

scispacy

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

59K 2K 253

biocypher

A unifying framework for biomedical research knowledge graphs

12K 304 51

bent

Biomedical Term Annotator

2K 9 1

pyradigm

Research data management in biomedical and machine learning applications

2K 30 12

fedbiomed

A collaborative learning framework for empowering biomedical research

2K 84 16

bio-epidemiology-ner

Recognize bio-medical entities from a text corpus

1K 133 9

pybiodatafuse

Python package for biodatafuse project.

1K 15 13

medpalm

MedPalm - Pytorch

537 432 59

optimuskg

A modern multimodal knowledge graph with type-specific metadata across biomedical domains.

500 64 6

node-synonymizer

Standalone Python client for the SRI Node Normalizer and Name Resolver APIs. Originally extracted from RTX-ARAX.

495 0 0

zensols-mimicsid

This repository contains the a Python package to automatically segment and identify sections of clinical notes, such as electronic health record (EHR) medical documents.

253 4 0

farabio

:robot: PyTorch toolkit for biomedical imaging :heart:

237 51 3

skill-to-mcp

Convert AI Skills (Claude Skills format) to MCP server resources

217 24 3

zensols-clinicamr

Clincial Domain Abstract Meaning Representation Graphs

207 0 0

refsig

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

112 1 2

pywinding

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

104 1 1

zensols-dsprov

Provenience of discharge summaries Pythonic access (BioNLP paper)

35 1 0