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

fields :class:`~<class 'property'>`#

All Bionty entity fields.

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

fuzzy_match(string, field='symbol', synonyms_field='synonyms', case_sensitive=True, return_ranked_results=False)#

Fuzzy matching of a given string against a Bionty field.

Parameters:

  • string – The input string to match against the field ontology values.

  • field – The BiontyField of ontology the input string is matching against.

  • synonyms_field – Also map against in the synonyms (If None, no mapping against synonyms).

  • case_sensitive – Whether the match is case sensitive.

  • return_ranked_results – Whether to return all entries ranked by matching ratios.

Return type:

DataFrame

Returns:

Best match of the input string.

Examples

>>> import bionty as bt
>>> celltype_bionty = bt.CellType()
>>> celltype_bionty.fuzzy_match("gamma delta T cell", celltype_bionty.name)
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