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/

The default indexer is ensembl_gene_id

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_versions.

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

Notes

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

Methods

curate(df, column=None, reference_id='ensembl_gene_id')

Curate index of passed DataFrame to conform with default identifier.

In addition to the .curate() in base class, this also performs alias mapping.

Parameters:

df – DataFrame with a column of identifiers

column: If column is None, checks the existing index for compliance with

the default identifier.

If column denotes an entity identifier, tries to map that identifier

to the default identifier.

reference_id: The type of identifier for mapping.

Return type:

DataFrame

Returns:

The input DataFrame with the curated index and a boolean __curated__ column that indicates compliance with the default identifier.

df()

DataFrame.

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 id.

Parameters:

field – The field to lookup the values for. Adapt this parameter to, for example, ‘ontology_id’ to lookup by ID. Defaults to ‘name’.

Returns:

A NamedTuple of lookup information of the entitys values.

Examples

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