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

  • source (Literal['ensembl'] | 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().

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.