bionty.Gene

class bionty.Gene(species='human', source=None, version=None, **kwargs)

Bases: Bionty

Gene.

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

Parameters:

• species – name of Species entity.

• source – The key of the source in the local.yml versions file. Get all available databases with bionty.display_available_sources.

• version – The version of the ontology. Typically a date or an actual version. Get available versions with bionty.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

source :class:`~<class 'property'>`

Name of the source.

species :class:`~<class 'property'>`

The name of Species Bionty.

version :class:`~<class 'property'>`

The name of version entity Bionty.

Methods

df()

DataFrame.

The default indexer is ensembl_gene_id

See ingestion: https://lamin.ai/docs/bionty-assets/ingest/ensembl-gene

Return type:

DataFrame

lookup(field='symbol')

Return an auto-complete object for the bionty field.

Parameters:

field – The field to lookup the values for. Defaults to ‘name’.

Return type:

tuple

Returns:

A NamedTuple of lookup information of the field values.

Examples

>>> import bionty as bt
>>> gene_lookout = bt.Gene().lookup()
>>> gene_lookout.TEF