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")
Release files for bionty-base 0.38.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| bionty_base-0.38.0.tar.gz | 62.3 kB | Without provenance | Details for bionty_base-0.38.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| bionty_base-0.38.0-py3-none-any.whl | Python 3 | none | any | Details for bionty_base-0.38.0-py3-none-any.whl |
Total release size: 102.9 kB
Release files / bionty_base-0.38.0.tar.gz
| Download URL | bionty_base-0.38.0.tar.gz |
|---|---|
| Size | 62.3 kB |
| Tags | Source |
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Release files / bionty_base-0.38.0-py3-none-any.whl
| Download URL | bionty_base-0.38.0-py3-none-any.whl |
|---|---|
| Size | 40.6 kB |
| Tags | Python 3 |
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