bionty_base.Organism

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

Bases: PublicOntology

Organism.

1. Organism ontology Edits of terms are coordinated and reviewed on: https://www.ensembl.org/index.html

Parameters:

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

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

Attributes

fields set

All PublicOntology entity fields.

organism property

The name of Organism.

source property

Name of the source.

version property

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 bt
>>> bt.Organism().df()