bionty_base.Gene#

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

Bases: PublicOntology

Gene.

1. Ensembl Edits of terms are coordinated and reviewed on: https://www.ensembl.org/

Parameters:

  • organism (Optional[Literal['human', 'mouse', 'saccharomyces cerevisiae']], default: None) – name of Organism entity.

  • source (Optional[Literal['ensembl']], 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().

Notes

Biotypes: https://www.ensembl.org/info/genome/genebuild/biotypes.html Gene Naming: https://www.ensembl.org/info/genome/genebuild/gene_names.html

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

map_legacy_ids(values)#

Convert legacy ids to current ids.