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()