lamindb.ULabel#

class lamindb.ULabel(name: str, description: Optional[str] = None, reference: Optional[str] = None, reference_type: Optional[str] = None)#

Bases: Registry, HasParents, CanValidate

Universal label ontology.

Parameters:

name – str A name.
description – str A description.
reference – Optional[str] = None For instance, an external ID or a URL.
reference_type – Optional[str] = None For instance, "url".

A ULabel record provides the easiest way to annotate a file or dataset with a label: "My project", "curated", or "Batch X":

>>> my_project = ULabel(name="My project")
>>> my_project.save()
>>> dataset.ulabels.add(my_project)

In some cases, a label is measured within a file or dataset a feature (a Feature record) denotes the column name in which the label is stored. For instance, the dataset might contain measurements across 2 organism of the Iris flower: "setosa" & "versicolor".

See Tutorial: Features & labels to learn more.

Note

If you work with complex entities like cell lines, cell types, tissues, etc., consider using the pre-defined biological registries in lnschema_bionty to label files & datasets.

If you work with biological samples, likely, the only sustainable way of tracking metadata, is to create a custom schema module.

See also

lamindb.Feature(): Dimensions of measurement for files & datasets.

Examples

Create a new label:

>>> my_project = ln.ULabel(name="My project")
>>> my_project.save()

Label a file without associating it to a feature:

>>> ulabel = ln.ULabel.filter(name="My project").one()
>>> file = ln.File("./myfile.csv")
>>> file.save()
>>> file.ulabels.add(ulabel)
>>> file.ulabels.list("name")
['My project']

Organize labels in a hierarchy:

>>> ulabels = ln.ULabel.lookup()  # create a lookup
>>> is_project = ln.ULabel(name="is_project")  # create a super-category `is_project`
>>> is_project.save()
>>> ulabels.my_project.parents.add(is_project)

Query by ULabel:

>>> ln.File.filter(ulabels=project).first()

Fields

id AutoField: Internal id, valid only in one DB instance.

uid CharField: A universal random id, valid across DB instances.

name CharField: Name or title of ulabel (required).

description TextField: A description (optional).

reference CharField: A reference like URL or external ID.

reference_type CharField: Type of reference, e.g., donor_id from Vendor X.

created_at DateTimeField: Time of creation of record.

updated_at DateTimeField: Time of last update to record.

created_by ForeignKey: Creator of record, a User.

parents ManyToManyField: Parent labels, useful to hierarchically group labels (optional).

Methods

classmethod from_values(values, **kwargs)#

Bulk create validated records by parsing values for an identifier (a name, an id, etc.).

Parameters:

values (TypeVar(ListLike, list, pd.Series, np.array)) – A list of values for an identifier, e.g. ["name1", "name2"].
field – A Registry field to look up, e.g., lb.CellMarker.name.
**kwargs – Additional conditions for creation of records, e.g., organism="human".

Return type:

List[ULabel]

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 with shared kwargs:

>>> pipelines = ln.Transform.from_values(["Pipeline 1", "Pipeline 2"], field="name",
...                                      type="pipeline", version="1")
>>> pipelines

Bulk create records from bionty:

>>> import lnschema_bionty as lb
>>> records = lb.CellType.from_values(["T cell", "B cell"], field="name")
>>> records