bionty.Phenotype

class bionty.Phenotype(name: str, ontology_id: str | None, abbr: str | None, synonyms: str | None, description: str | None, parents: list[Phenotype], source: Source | None)

Bases: BioRecord, TracksRun, TracksUpdates

Phenotypes - Human Phenotype, Phecodes, Mammalian Phenotype, Zebrafish Phenotype.

Notes

For more info, see tutorials Manage biological registries and Phenotype.

Bulk create Phenotype records via from_values().

Examples

>>> record = bionty.Phenotype.from_source(name="Arachnodactyly")
>>> record.save()

Attributes

DoesNotExist = <class 'bionty.models.Phenotype.DoesNotExist'>
Meta = <class 'bionty.models.BioRecord.Meta'>
MultipleObjectsReturned = <class 'bionty.models.Phenotype.MultipleObjectsReturned'>
artifacts: Artifact

Artifacts linked to the phenotype.

children

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

created_by: User

Creator of record.

created_by_id

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

objects = <django.db.models.manager.Manager object>
parents: Phenotype

Parent phenotype records.

property pk
run: Run | None

Last run that created or updated the record.

run_id
source

Source this record associates with.

source_id

Class methods

classmethod add_source(source, currently_used=True)

Configure a source of the entity.

Return type:

Source

classmethod from_source(*, mute=False, **kwargs)

Create a record or records from source based on a single field value.

Return type:

BioRecord | list[BioRecord] | None

Notes

For more info, see tutorial bionty

Bulk create records via from_values().

Examples

Create a record by passing a field value:

>>> record = bionty.Gene.from_source(symbol="TCF7", organism="human")

Create a record from non-default source:

>>> source = bionty.Source.get(entity="CellType", source="cl", version="2022-08-16")  # noqa
>>> record = bionty.CellType.from_source(name="T cell", source=source)
classmethod import_source(source=None, ontology_ids=None, organism=None, ignore_conflicts=True)

Bulk save records from a Bionty ontology.

Use this method to initialize your registry with public ontology.

Parameters:

  • ontology_ids (list[str] | None, default: None) – List of ontology ids to save.

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

  • source (Source | None, default: None) – Source record to import records from.

  • ignore_conflicts (bool, default: True) – Whether to ignore conflicts during bulk record creation.

Examples

>>> bionty.CellType.import_source()
classmethod inspect(values, field=None, *, mute=False, organism=None, source=None)

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.

Return type:

InspectResult

See also

validate()

Examples

>>> import bionty as bt
>>> bt.settings.organism = "human"
>>> ln.save(bt.Gene.from_values(["A1CF", "A1BG", "BRCA2"], field="symbol"))
>>> gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
>>> result = bt.Gene.inspect(gene_symbols, field=bt.Gene.symbol)
>>> result.validated
['A1CF', 'A1BG']
>>> result.non_validated
['FANCD1', 'FANCD20']
classmethod public(organism=None, source=None)

The corresponding bionty.base.PublicOntology object.

Note that the source is auto-configured and tracked via bionty.Source. :rtype: PublicOntology | StaticReference

See also

Access public ontologies

Examples

>>> celltype_pub = bionty.CellType.public()
>>> celltype_pub
PublicOntology
Entity: CellType
Organism: all
Source: cl, 2023-04-20
#terms: 2698
classmethod standardize(values, field=None, *, return_field=None, return_mapper=False, case_sensitive=False, mute=False, public_aware=True, keep='first', synonyms_field='synonyms', organism=None, source=None)

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.

  • public_aware (bool, default: True) – Whether to standardize from Bionty reference. Defaults to True for Bionty 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.

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.

Examples

>>> import bionty as bt
>>> bt.settings.organism = "human"
>>> ln.save(bt.Gene.from_values(["A1CF", "A1BG", "BRCA2"], field="symbol"))
>>> gene_synonyms = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
>>> standardized_names = bt.Gene.standardize(gene_synonyms)
>>> standardized_names
['A1CF', 'A1BG', 'BRCA2', 'FANCD20']
classmethod validate(values, field=None, *, mute=False, organism=None, source=None)

Validate values against existing values of a string field.

Note this is strict 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.

Return type:

ndarray

Returns:

A vector of booleans indicating if an element is validated.

See also

inspect()

Examples

>>> import bionty as bt
>>> bt.settings.organism = "human"
>>> ln.save(bt.Gene.from_values(["A1CF", "A1BG", "BRCA2"], field="symbol"))
>>> gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
>>> bt.Gene.validate(gene_symbols, field=bt.Gene.symbol)
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.

Examples

>>> import bionty as bt
>>> bt.CellType.from_source(name="T cell").save()
>>> lookup = bt.CellType.lookup()
>>> record = lookup.t_cell
>>> record.synonyms
'T-cell|T lymphocyte|T-lymphocyte'
>>> record.add_synonym("T cells")
>>> record.synonyms
'T cells|T-cell|T-lymphocyte|T lymphocyte'
async adelete(using=None, keep_parents=False)
async arefresh_from_db(using=None, fields=None, from_queryset=None)
async asave(*args, force_insert=False, force_update=False, using=None, update_fields=None)
clean()

Hook for doing any extra model-wide validation after clean() has been called on every field by self.clean_fields. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

clean_fields(exclude=None)

Clean all fields and raise a ValidationError containing a dict of all validation errors if any occur.

date_error_message(lookup_type, field_name, unique_for)
delete()

Delete.

Return type:

None

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:

list[Record]

Returns:

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

Notes

For more info, see tutorial: Manage biological registries.

Examples

Bulk create from non-validated values will log warnings & returns empty list:

>>> ulabels = ln.ULabel.from_values(["benchmark", "prediction", "test"], field="name")
>>> assert len(ulabels) == 0

Bulk create records from validated values returns the corresponding existing records:

>>> ln.save([ln.ULabel(name=name) for name in ["benchmark", "prediction", "test"]])
>>> ulabels = ln.ULabel.from_values(["benchmark", "prediction", "test"], field="name")
>>> assert len(ulabels) == 3

Bulk create records from public reference:

>>> import bionty as bt
>>> records = bt.CellType.from_values(["T cell", "B cell"], field="name")
>>> records
get_constraints()
get_deferred_fields()

Return a set containing names of deferred fields for this instance.

prepare_database_save(field)
query_children()

Query children in an ontology.

Return type:

QuerySet

query_parents()

Query parents in an ontology.

Return type:

QuerySet

refresh_from_db(using=None, fields=None, from_queryset=None)

Reload field values from the database.

By default, the reloading happens from the database this instance was loaded from, or by the read router if this instance wasn’t loaded from any database. The using parameter will override the default.

Fields can be used to specify which fields to reload. The fields should be an iterable of field attnames. If fields is None, then all non-deferred fields are reloaded.

When accessing deferred fields of an instance, the deferred loading of the field will call this method.

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

Examples

>>> import bionty as bt
>>> bt.CellType.from_source(name="T cell").save()
>>> lookup = bt.CellType.lookup()
>>> record = lookup.t_cell
>>> record.synonyms
'T-cell|T lymphocyte|T-lymphocyte'
>>> record.remove_synonym("T-cell")
'T lymphocyte|T-lymphocyte'
save(*args, **kwargs)

Save the record and its parents recursively.

Return type:

BioRecord

save_base(raw=False, force_insert=False, force_update=False, using=None, update_fields=None)

Handle the parts of saving which should be done only once per save, yet need to be done in raw saves, too. This includes some sanity checks and signal sending.

The ‘raw’ argument is telling save_base not to save any parent models and not to do any changes to the values before save. This is used by fixture loading.

serializable_value(field_name)

Return the value of the field name for this instance. If the field is a foreign key, return the id value instead of the object. If there’s no Field object with this name on the model, return the model attribute’s value.

Used to serialize a field’s value (in the serializer, or form output, for example). Normally, you would just access the attribute directly and not use this method.

set_abbr(value)

Set value for abbr field and add to synonyms.

Parameters:

value (str) – A value for an abbreviation.

See also

add_synonym()

Examples

>>> import bionty as bt
>>> bt.ExperimentalFactor.from_source(name="single-cell RNA sequencing").save()
>>> scrna = bt.ExperimentalFactor.get(name="single-cell RNA sequencing")
>>> scrna.abbr
None
>>> scrna.synonyms
'single-cell RNA-seq|single-cell transcriptome sequencing|scRNA-seq|single cell RNA sequencing'
>>> scrna.set_abbr("scRNA")
>>> scrna.abbr
'scRNA'
>>> scrna.synonyms
'scRNA|single-cell RNA-seq|single cell RNA sequencing|single-cell transcriptome sequencing|scRNA-seq'
>>> scrna.save()
unique_error_message(model_class, unique_check)
validate_constraints(exclude=None)
validate_unique(exclude=None)

Check unique constraints on the model and raise ValidationError if any failed.

view_parents(field=None, with_children=False, distance=5)

View parents in an ontology.

Parameters:

  • field (str | DeferredAttribute | None, default: None) – Field to display on graph

  • with_children (bool, default: False) – Whether to also show children.

  • distance (int, default: 5) – Maximum distance still shown.

Ontological hierarchies: ULabel (project & sub-project), CellType (cell type & subtype).

Examples

>>> import bionty as bt
>>> bt.Tissue.from_source(name="subsegmental bronchus").save()
>>> record = bt.Tissue.get(name="respiratory tube")
>>> record.view_parents()
>>> tissue.view_parents(with_children=True)