Bionty.
Project description
Bionty
Access public biological ontologies.
Installation
Bionty is a Python package available for
pip install bionty
Entities
Gene- Ensembl, NCBI GeneProtein- UniprotOrganism- Ensembl Species. NCBI TaxonomyCellLine- Cell Line OntologyCellType- Cell OntologyCellMarker- CellMarkerTissue- UberonDisease- Mondo, Human DiseasePhenotype- Human Phenotype, Phecodes, PATO, Mammalian Phenotype, Zebrafish PhenotypePathway- Gene Ontology, Pathway OntologyExperimentalFactor- Experimental Factor OntologyDevelopmentalStage- Human Developmental Stages, Mouse Developmental StagesDrug- Drug OntologyEthnicity- Human Ancestry OntologyBFXPipeline- largely based on nf-coreBioSample- NCBI BioSample attributes
Check out sources.yaml for details.
Didn't see your favorite source or version? Bionty is extendable!
Entity versions
import bionty as bt
# display currently used sources
bt.display_currently_used_sources()
# display all managed sources
bt.display_available_sources()
# local yaml file specifying all managed sources
bt.LOCAL_SOURCES
# access to the Mondo ontology
disease = bt.Disease(source="mondo")
# access to the Human Disease ontology
disease = bt.Disease(source="doid", version="2023-01-30")
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