lamindb.models.CanCurate

class lamindb.models.CanCurate

Bases: object

Base class providing Record-based validation.

Class methods

classmethod from_values(values, field=None, create=False, organism=None, source=None, mute=False)

Bulk create validated records by parsing values for an identifier such as a name or an id).

Parameters:

  • values (list[str] | Series | array) – A list of values for an identifier, e.g. ["name1", "name2"].

  • field (str | DeferredAttribute | None, default: None) – A Record field to look up, e.g., bt.CellMarker.name.

  • create (bool, default: False) – Whether to create records if they don’t exist.

  • organism (Record | str | None, default: None) – A bionty.Organism name or record.

  • source (Record | None, default: None) – A bionty.Source record to validate against to create records for.

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

Return type:

RecordList

Returns:

A list of validated records. For bionty registries. Also returns knowledge-coupled records.

Notes

For more info, see tutorial: Manage biological registries.

Example:

import bionty as bt

# Bulk create from non-validated values will log warnings & returns empty list
ulabels = ln.ULabel.from_values(["benchmark", "prediction", "test"])
assert len(ulabels) == 0

# Bulk create records from validated values returns the corresponding existing records
ulabels = ln.ULabel.from_values(["benchmark", "prediction", "test"], create=True).save()
assert len(ulabels) == 3

# Bulk create records from public reference
bt.CellType.from_values(["T cell", "B cell"]).save()
classmethod inspect(values, field=None, *, mute=False, organism=None, source=None, strict_source=False)

Inspect if values are mappable to a field.

Being mappable means that an exact match exists.

Parameters:

  • values (list[str] | Series | array) – Values that will be checked against the field.

  • field (str | DeferredAttribute | None, default: None) – The field of values. 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 mute logging.

  • organism (str | Record | None, default: None) – An Organism name or record.

  • source (Record | None, default: None) – A bionty.Source record that specifies the version to inspect against.

  • strict_source (bool, default: False) – Determines the validation behavior against records in the registry. - If False, validation will include all records in the registry, ignoring the specified source. - If True, validation will only include records in the registry that are linked to the specified source. Note: this parameter won’t affect validation against public sources.

Return type:

InspectResult

See also

validate()

Example:

import bionty as bt

# save some gene records
bt.Gene.from_values(["A1CF", "A1BG", "BRCA2"], field="symbol", organism="human").save()

# inspect gene symbols
gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
result = bt.Gene.inspect(gene_symbols, field=bt.Gene.symbol, organism="human")
assert result.validated == ["A1CF", "A1BG"]
assert result.non_validated == ["FANCD1", "FANCD20"]
classmethod standardize(values, field=None, *, return_field=None, return_mapper=False, case_sensitive=False, mute=False, source_aware=True, keep='first', synonyms_field='synonyms', organism=None, source=None, strict_source=False)

Maps input synonyms to standardized names.

Parameters:

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

  • field (str | DeferredAttribute | None, default: None) – The field representing the standardized names.

  • return_field (str | DeferredAttribute | None, default: None) – The field to return. Defaults to field.

  • return_mapper (bool, default: False) – If True, returns {input_value: standardized_name}.

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

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

  • source_aware (bool, default: True) – Whether to standardize from public source. Defaults to True for BioRecord registries.

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

    When a synonym maps to multiple names, determines which duplicates to mark as pd.DataFrame.duplicated: - "first": returns the first mapped standardized name - "last": returns the last mapped standardized name - False: returns all mapped standardized name.

    When keep is False, the returned list of standardized names will contain nested lists in case of duplicates.

    When a field is converted into return_field, keep marks which matches to keep when multiple return_field values map to the same field value.

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

  • organism (str | Record | None, default: None) – An Organism name or record.

  • source (Record | None, default: None) – A bionty.Source record that specifies the version to validate against.

  • strict_source (bool, default: False) – Determines the validation behavior against records in the registry. - If False, validation will include all records in the registry, ignoring the specified source. - If True, validation will only include records in the registry that are linked to the specified source. Note: this parameter won’t affect validation against public sources.

Return type:

list[str] | dict[str, 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.

See also

add_synonym()

Add synonyms.

remove_synonym()

Remove synonyms.

Example:

import bionty as bt

# save some gene records
bt.Gene.from_values(["A1CF", "A1BG", "BRCA2"], field="symbol", organism="human").save()

# standardize gene synonyms
gene_synonyms = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
bt.Gene.standardize(gene_synonyms)
#> ['A1CF', 'A1BG', 'BRCA2', 'FANCD20']
classmethod validate(values, field=None, *, mute=False, organism=None, source=None, strict_source=False)

Validate values against existing values of a string field.

Note this is strict_source validation, only asserts exact matches.

Parameters:

  • values (list[str] | Series | array) – Values that will be validated against the field.

  • field (str | DeferredAttribute | None, default: None) – The field of values. 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 mute logging.

  • organism (str | Record | None, default: None) – An Organism name or record.

  • source (Record | None, default: None) – A bionty.Source record that specifies the version to validate against.

  • strict_source (bool, default: False) – Determines the validation behavior against records in the registry. - If False, validation will include all records in the registry, ignoring the specified source. - If True, validation will only include records in the registry that are linked to the specified source. Note: this parameter won’t affect validation against public sources.

Return type:

ndarray

Returns:

A vector of booleans indicating if an element is validated.

See also

inspect()

Example:

import bionty as bt

bt.Gene.from_values(["A1CF", "A1BG", "BRCA2"], field="symbol", organism="human").save()

gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
bt.Gene.validate(gene_symbols, field=bt.Gene.symbol, organism="human")
#> array([ True,  True, False, False])

Methods

add_synonym(synonym, force=False, save=None)

Add synonyms to a record.

Parameters:

  • synonym (str | list[str] | Series | array) – The synonyms to add to the record.

  • force (bool, default: False) – Whether to add synonyms even if they are already synonyms of other records.

  • save (bool | None, default: None) – Whether to save the record to the database.

See also

remove_synonym()

Remove synonyms.

Example:

import bionty as bt

# save "T cell" record
record = bt.CellType.from_source(name="T cell").save()
record.synonyms
#> "T-cell|T lymphocyte|T-lymphocyte"

# add a synonym
record.add_synonym("T cells")
record.synonyms
#> "T cells|T-cell|T-lymphocyte|T lymphocyte"
remove_synonym(synonym)

Remove synonyms from a record.

Parameters:

synonym (str | list[str] | Series | array) – The synonym values to remove.

See also

add_synonym()

Add synonyms

Example:

import bionty as bt

# save "T cell" record
record = bt.CellType.from_source(name="T cell").save()
record.synonyms
#> "T-cell|T lymphocyte|T-lymphocyte"

# remove a synonym
record.remove_synonym("T-cell")
record.synonyms
#> "T lymphocyte|T-lymphocyte"
set_abbr(value)

Set value for abbr field and add to synonyms.

Parameters:

value (str) – A value for an abbreviation.

See also

add_synonym()

Example:

import bionty as bt

# save an experimental factor record
scrna = bt.ExperimentalFactor.from_source(name="single-cell RNA sequencing").save()
assert scrna.abbr is None
assert scrna.synonyms == "single-cell RNA-seq|single-cell transcriptome sequencing|scRNA-seq|single cell RNA sequencing"

# set abbreviation
scrna.set_abbr("scRNA")
assert scrna.abbr == "scRNA"
# synonyms are updated
assert scrna.synonyms == "scRNA|single-cell RNA-seq|single cell RNA sequencing|single-cell transcriptome sequencing|scRNA-seq"