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#

Gene - Ensembl, NCBI Gene, HGNC, MGI
Protein - Uniprot
Species - NCBI Taxonomy, Ensembl Species
CellLine - Cell Line Ontology
CellType - Cell Ontology
CellMarker - CellMarker
Tissue - Uberon
Disease - Mondo, Human Disease
Phenotype - Human Phenotype
Pathway - Gene Ontology, Pathway Ontology
Readout - Experimental Factor Ontology
BFXPipeline - largely based on nf-core

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!