bionty.base.BioSample

class bionty.base.BioSample(organism=None, source=None, version=None, **kwargs)

Bases: PublicOntology

BioSample attributes.

1. NCBI BioSample Attributes https://www.ncbi.nlm.nih.gov/biosample/docs/attributes

Parameters:

  • organism (Literal['all'] | None, default: None) – name of Organism entity.

  • source (Literal['ncbi'] | None, default: None) – The name of the source in the sources.yaml file. Get available sources with .display_available_sources().

  • version (Literal['2023-09'] | None, default: None) – The version of the ontology. Typically a date or an actual version. Get latest versions with .display_available_sources().

Attributes

property fields: set

All PublicOntology entity fields.

property organism

The name of Organism.

property source

Name of the source.

property version

Version of the source.

Methods

to_pronto(mute=False)

The Pronto Ontology object.

See: https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html

Return type:

bionty.base._ontology.Ontology

to_dataframe()

Pandas DataFrame of the ontology.

Return type:

DataFrame

Returns:

A Pandas DataFrame of the ontology.

Example:

import bionty.base as bt_base

bt_base.Gene().to_dataframe()
validate(values, field, *, mute=False, **kwargs)

Validate a list of values against a field of entity reference.

Parameters:

  • values (Iterable) – Identifiers that will be checked against the field.

  • field (PublicOntologyField) – The PublicOntologyField of the ontology to compare against. Examples are ‘ontology_id’ to map against the source ID or ‘name’ to map against the ontologies field names.

  • mute (bool, default: False) – Whether to suppress logging. Defaults to False.

  • kwargs – Used for backwards compatibility and return types.

Return type:

ndarray

Returns:

A boolean array indicating compliance validation.

Example:

import bionty.base as bt_base

public = bt_base.Gene()
gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
public.validate(gene_symbols, field=public.symbol)
inspect(values, field, *, mute=False, **kwargs)

Inspect a list of values against a field of entity reference.

Parameters:

  • values (Iterable) – Identifiers that will be checked against the field.

  • field (PublicOntologyField) – The PublicOntologyField of the ontology to compare against. Examples are ‘ontology_id’ to map against the source ID or ‘name’ to map against the ontologies field names.

  • return_df – Whether to return a Pandas DataFrame.

  • mute (bool, default: False) – Whether to suppress logging. Defaults to False.

  • kwargs – Used for backwards compatibility and return types.

Return type:

bionty.base.dev.InspectResult

Returns:

  • A Dictionary of “validated” and “not_validated” identifiers

  • If return_df: A DataFrame indexed by identifiers with a boolean

    __validated__ column indicating compliance validation.

Example:

import bionty.base as bt_base

public = bt_base.Gene()
gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
public.inspect(gene_symbols, field=public.symbol)
standardize(values, field=None, *, return_field=None, return_mapper=False, case_sensitive=False, mute=False, keep='first', synonyms_field='synonyms')

Convert into standardized names.

Parameters:

  • values (Iterable) – Iterable Synonyms that will be standardized.

  • field (PublicOntologyField | str | None, default: None) – Optional[str] The field representing the standardized names.

  • return_field (str, default: None) – Optional[str] The field to return. Defaults to field.

  • return_mapper (bool, default: False) – bool = False If True, returns {input_synonym1: standardized_name1}.

  • case_sensitive (bool, default: False) – bool = False Whether the mapping is case sensitive.

  • keep (Literal['first', 'last', False], default: 'first') –

    {‘first’, ‘last’, False}, default ‘first’. When a synonym maps to multiple standardized values, determines which duplicates to mark as pandas.DataFrame.duplicated.

    • ”first”: returns the first mapped standardized value

    • ”last”: returns the last mapped standardized value

    • False: returns all mapped standardized value

  • mute (bool, default: False) – Whether to mute logging. Defaults to False.

  • synonyms_field (PublicOntologyField | str, default: 'synonyms') – str = "synonyms" A field containing the concatenated synonyms.

Return type:

dict[str, str] | list[str]

Returns:

If return_mapper is False – a list of standardized names. Otherwise, a dictionary of mapped values with mappable synonyms as keys and standardized names as values.

Example:

import bionty.base as bt_base

public = bt_base.Gene()
gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
standardized_symbols = public.standardize(gene_symbols, public.symbol)
lookup(field=None)

An auto-complete object for a PublicOntology field.

Parameters:

field (PublicOntologyField | str | None, default: None) – The field to lookup the values for. Defaults to ‘name’.

Return type:

tuple

Returns:

A NamedTuple of lookup information of the field values.

Example:

import bionty.base as bt_base

lookup = bt_base.CellType().lookup()
lookup.cd103_positive_dendritic_cell
lookup_dict = lookup.dict()
lookup['CD103-positive dendritic cell']
search(string, *, field=None, limit=None, case_sensitive=False)

Search a given string against a PublicOntology field or fields.

Parameters:

  • string (str) – The input string to match against the field values.

  • field (PublicOntologyField | str | list[PublicOntologyField | str], default: None) – The PublicOntologyField or several fileds of the ontology the input string is matching against. Search all fields containing strings by default.

  • limit (int | None, default: None) – Maximum amount of top results to return. If None, return all results.

  • case_sensitive (bool, default: False) – Whether the match is case sensitive.

Returns:

Ranked search results.

Example:

import bionty.base as bt_base

public = bt_base.CellType()
public.search("gamma delta T cell")
diff(compare_to, **kwargs)

Determines a diff between two PublicOntology objects’ ontologies.

Parameters:

  • compare_to (PublicOntology) – PublicOntology object that must be of the same class as the calling object.

  • kwargs – Are passed to pd.DataFrame.compare()

Return type:

tuple[DataFrame, DataFrame]

Returns:

A tuple of two DataFrames –

  1. New entries.

  2. A pd.DataFrame.compare result which denotes all changes in self and other.

Example:

import bionty.base as bt_base

public_1 = bt_base.Disease(source="mondo", version="2023-04-04")
public_2 = bt_base.Disease(source="mondo", version="2023-04-04")
new_entries, modified_entries = public_1.diff(public_2)
print(new_entries.head())
print(modified_entries.head())