bionty.base¶

Bionty base is a standalone version of Bionty without lamindb support.

Overview¶

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

>>> pip install bionty

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()

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

`Organism`([organism, 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.

[Pronto Ontology objects](https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html) can be accessed via {entity}.to_pronto():

bt_base.Gene().to_pronto()

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

`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`

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

Interface with ontologies via pronto.