Biomedical Python Packages

scispacy

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

biocypher

A unifying framework for biomedical research knowledge graphs

bent

Biomedical Term Annotator

bio-epidemiology-ner

Recognize bio-medical entities from a text corpus

optimuskg

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

umlsmatch

Python-native clinical NLP pipeline for clinical concept extraction

bmlib

Shared Python library for biomedical literature tools — LLM abstraction, quality assessment, transparency analysis, full-text retrieval, publication ingestion, and database utilities.

refsig

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

fedbiomed

A collaborative learning framework for empowering biomedical research

medpalm

Towards Generalist Biomedical AI

pyradigm

Research data management in biomedical and machine learning applications

skill-to-mcp

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

pybiodatafuse

Python package for biodatafuse project.

zensols-mimicsid

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

netbox-biomed

NetBox plugin - cartographie des equipements biomedicaux connectes : plateaux techniques, equipements, flux et posture cyber

node-synonymizer

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

farabio

:robot: PyTorch toolkit for biomedical imaging :heart:

pywinding

pywinding - A simulation tool for the design and evaluation of induction microcoils

meridian-rag

A from-scratch grounded RAG engine over biomedical literature (PubMed). Every ML component trained in-house; every answer cited, verified, or refused. Not medical advice.

sciveris

Sciveris re-executes a study and checks whether the finding is real — data leakage, batch/site confounds, effect-size inflation, p-hacking. Latin: "you will have known."

zensols-clinicamr

Clincial Domain Abstract Meaning Representation Graphs

zensols-dsprov

Provenience of discharge summaries Pythonic access (BioNLP paper)