Bionty: Data model generator for biology.
Project description
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, MGIProtein- UniprotSpecies- NCBI Taxonomy, Ensembl SpeciesCellLine- Cell Line OntologyCellType- Cell OntologyCellMarker- CellMarkerTissue- UberonDisease- Mondo, Human DiseasePhenotype- Human PhenotypePathway- Gene Ontology, Pathway OntologyReadout- Experimental Factor OntologyBFXPipeline- largely based on nf-core
Check out sources.yaml for details.
Installation
Bionty is a Python package available for
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.
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