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Bionty: Data model generator for biology.

Project description

Stars Coverage pypi

Bionty: Basic biological entities

Access public & custom ontologies with auto-complete. Map synonyms with ease.

To manage in-house bioregistries along with ontologies, see lnschema_bionty.

Out-of-the-box ontologies

Check out sources.yaml for details.

Installation

Bionty is a Python package available for pyversions

pip install bionty

Look up ontology records with auto-complete

import bionty as bt

gene = bt.Gene()
gene.lookup().LNMA

Track ontology sources

# Display all managed versions
bt.display_available_sources()

# Access to the Mondo ontology
disease = bt.Disease(database="mondo")

# Access to the Human Disease ontology
disease = bt.Disease(database="doid", version="2023-01-30")

Didn't see your favorite source or version? Bionty is extendable!

Documentation

Read the docs.

Project details


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