bionty.Gene#

class bionty.Gene(species='human', database=None, version=None)#

Bases: Entity

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.

  • database – The key of the database 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. :rtype: DataFrame

  • 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.

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

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

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.