bionty.Organism

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

Bases: Bionty

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 bionty.display_available_sources.

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

Attributes

fields property

All Bionty entity fields.

organism property

The name of Organism Bionty.

source property

Name of the source.

version property

The name of version entity Bionty.

Methods

df()

Pandas DataFrame of the ontology.

Return type:

DataFrame

Returns:

A Pandas DataFrame of the ontology.

Examples

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