Ontologies Python Packages

lamindb

Open-source data framework for biology. Query, trace & validate with a lineage-native lakehouse that supports bio-formats, registries & ontologies. 🍊YC S22

ontoportal-client

🎡 Unified access to OntoPortal instances like BioPortal, AgroPortal, and EcoPortal

ols-client

🎡 Unified access to OLS instances like from the EBI and TIB

lamindb-core

Open-source data framework for biology. Query, trace & validate with a lineage-native lakehouse that supports bio-formats, registries & ontologies. 🍊YC S22

naas-abi-marketplace

AI Operating System - Build your own AI using ontologies as the unifying field connecting data, models, workflows, and systems.

naas-abi

AI Operating System - Build your own AI using ontologies as the unifying field connecting data, models, workflows, and systems.

bel-resources

Utilities for BEL resource files.

naas-abi-core

AI Operating System - Build your own AI using ontologies as the unifying field connecting data, models, workflows, and systems.

pyobo

📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

naas-abi-cli

AI Operating System - Build your own AI using ontologies as the unifying field connecting data, models, workflows, and systems.

bio2bel

A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)

nxontology

NetworkX-based Python library for representing ontologies

ssslm

A simple standard for sharing literal mappings (SSSLM)

emmontopy

Library for representing and working with ontologies in Python

linkml-owl

Extension of LinkML runtime for converting instances of LinkML classes to OWL (classes or instances)

ontolearner

OntoLearner: A Modular Python Library for Ontology Learning with LLMs https://pypi.org/project/OntoLearner/

omnipy

Omnipy is a high level Python library for type-driven data wrangling and scalable workflow orchestration (under development)

emmo

Python reference API for the Europeean Materials & Modelling Ontology

cello-classify

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

deeponto

A package for ontology engineering with deep learning and language models.

mowl-borg

mOWL: Machine Learning library with Ontologies

interpretme

An interpretable machine learning pipeline over knowledge graphs

onto2nx

A package for parsing ontologies in the OWL and OBO format into NetworkX graphs

pkt-kg

PheKnowLator: Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models