bionty.base

Access to public ontologies.

bionty.base is the read-only interface for public ontology that underlies bionty and doesn’t require a lamindb instance.

Import the package:

>>> import bionty.base as bt_base

Access public ontologies:

>>> genes = bt_base.Gene()

Get a DataFrame of all available values:

>>> genes.df()

Entities

Bionty base provides access to several entities, most of which are also supported by Bionty.

Organism([taxa, source, version])	Organism.
Gene([organism, source, version])	Gene.
Protein([organism, source, version])	Protein.
CellMarker([organism, source, version])	Cell markers.
CellType([organism, source, version])	Cell type ontologies.
CellLine([organism, source, version])	Cell line.
Tissue([organism, source, version])	Tissue.
Disease([organism, source, version])	Disease ontologies.
Phenotype([organism, source, version])	Phenotype.
Pathway([organism, source, version])	Pathway.
ExperimentalFactor([organism, source, version])	Experimental Factor.
DevelopmentalStage([organism, source, version])	Developmental Stage.
Drug([organism, source, version])	Drug ontologies.
Ethnicity([organism, source, version])	Ethnicity.
BFXPipeline([organism, source, version])	Bioinformatics pipelines.
BioSample([organism, source, version])	BioSample attributes.

Base class

Pronto Ontology objects can be accessed via {entity}.to_pronto().

PublicOntology([source, version, organism, ...])	PublicOntology object.
PublicOntologyField(parent, name)	Field of a PublicOntology model.

Ontology sources

display_available_sources()	Displays all available sources.
display_currently_used_sources()	Displays all currently used sources.
reset_sources([confirm])	Reset local bionty sources file.
settings

Pronto Ontology

Ontology([handle, import_depth, timeout, ...])

Interface with ontologies via pronto.