bionty.base.Organism

class bionty.base.Organism(organism=None, source=None, version=None, **kwargs)

Bases: PublicOntology

Organism.

1. Organism ontology https://www.ensembl.org/index.html

Parameters:

• source (Literal['ensembl', 'ncbitaxon'] | None, default: None) – The key of the source in the local.yml versions file. Get all available databases with .display_available_sources().

• version (str | None, default: None) – The version of the ontology. Typically a date or an actual version. Get available versions with .display_available_sources().

Attributes

property fields: set

All PublicOntology entity fields.

property organism

The name of Organism.

property source

Name of the source.

property version

Version of the source.

Methods

df()

Pandas DataFrame of the ontology.

Return type:

DataFrame

Returns:

A Pandas DataFrame of the ontology.

Examples

>>> import bionty.base as bionty_base
>>> bt.Organism().df()