bionty.Bionty

class bionty.Bionty(source, version=None, species=None, *, reference_id=None, synonyms_field=None, include_id_prefixes=None, include_name_prefixes=None, exclude_id_prefixes=None, exclude_name_prefixes=None, **kwargs)

Bases: object

Biological entity as an Bionty.

See Guide for background.

Attributes

database

Name of the source.

ontology

The Pronto Ontology object.

species

The name of Species Bionty.

version

The name of version entity Bionty.

Methods

curate(df, column=None, reference_id=None, case_sensitive=True)

Curate index of passed DataFrame to conform with default identifier.

• If target_column is None, checks the existing index for compliance with the default identifier.

• If target_column denotes an entity identifier, tries to map that identifier to the default identifier.

Parameters:

• df – The input Pandas DataFrame to curate.

• column – The column in the passed Pandas DataFrame to curate.

• reference_id – The reference column in the ontology Pandas DataFrame. ‘Defaults to ontology_id’.

• case_sensitive – Whether the curation should be case sensitive or not. Defaults to True.

Return type:

DataFrame

Returns:

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

df()

Pandas DataFrame.

Return type:

DataFrame

inspect(identifiers, reference_id, return_df=False)

Inspect if a list of identifiers are mappable to the entity reference.

Parameters:

• identifiers – Identifiers that will be checked against the Ontology.

• reference_id – The BiontyField of the ontology to compare against. Examples are ‘ontology_id’ to map against the ontology ID or ‘name’ to map against the ontologies field names.

• return_df – Whether to return a Pandas DataFrame.

Return type:

Union[DataFrame, dict[str, list[str]]]

Returns:

• A Dictionary that maps the input ontology (keys) to the ontology field (values)

• If specified A Pandas DataFrame with the curated index and a boolean __curated__ column that indicates compliance with the default identifier.

lookup(field='name')

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’.

Return type:

tuple

Returns:

A NamedTuple of lookup information of the entitys values.

map_synonyms(identifiers, reference_id, *, synonyms_field=None, return_mapper=False)

Maps input identifiers against Ontology synonyms.

Parameters:

• identifiers – Identifiers that will be mapped against the Ontology.

• reference_id – The BiontyField of the ontology to compare against. Examples are ‘ontology_id’ to map against the ontology ID or ‘name’ to map against the ontologies field names.

• return_mapper – Whether to return a dictionary with keys mappable identifiers to values mapped reference_id values.

Return type:

Union[Dict[str, str], List[str]]

Returns:

• A list of mapped reference_id values if return_mapper is False.

• A dictionary of mapped values with mappable identifiers as keys and values mapped to reference_id as values if return_mapper is True.