Access public biological ontologies.
Bionty-base is a Python package available for
pip install bionty-base
-
Gene
- Ensembl, NCBI Gene -
Protein
- Uniprot -
Organism
- Ensembl Species. NCBI Taxonomy -
CellLine
- Cell Line Ontology -
CellType
- Cell Ontology -
CellMarker
- CellMarker -
Tissue
- Uberon -
Disease
- Mondo, Human Disease, ICD -
Phenotype
- Human Phenotype, Phecodes, PATO, Mammalian Phenotype, Zebrafish Phenotype -
Pathway
- Gene Ontology, Pathway Ontology -
ExperimentalFactor
- Experimental Factor Ontology -
DevelopmentalStage
- Human Developmental Stages, Mouse Developmental Stages -
Drug
- Drug Ontology -
Ethnicity
- Human Ancestry Ontology -
BFXPipeline
- largely based on nf-core -
BioSample
- NCBI BioSample attributes
Check out sources.yaml for details.
Didn't see your favorite source or version? Bionty is extendable!
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")