Bionty.
Project description
bionty-base
Access public biological ontologies.
Installation
Bionty-base is a Python package available for
pip install bionty-base
Entities
Gene
- Ensembl, NCBI GeneProtein
- UniprotOrganism
- Ensembl Species. NCBI TaxonomyCellLine
- Cell Line OntologyCellType
- Cell OntologyCellMarker
- CellMarkerTissue
- UberonDisease
- Mondo, Human Disease, ICDPhenotype
- 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_base 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")
Project details
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