bionty.Source

class bionty.Source(entity: str, organism: str, name: str, version: str, currently_used: bool, description: str | None, url: str | None, md5: str | None, source_website: str | None)

Bases: Record, TracksRun, TracksUpdates

Versions of ontology sources.

Warning

Do not modify the records unless you know what you are doing!

Simple fields

uid: str

A universal id (hash of selected field).

entity: str

Entity class name.

organism: str

Organism name, use ‘all’ if unknown or none applied.

name: str

Source name, short form, CURIE prefix for ontologies.

version: str

Version of the source.

in_db: bool

Whether this ontology has be added to the database.

currently_used: bool

Whether this record is currently used.

description: str | None

Source full name, long form.

url: str | None

URL of the source file.

md5: str | None

Hash md5 of the source file.

source_website: str | None

Website of the source.

created_at: datetime

Time of creation of record.

updated_at: datetime

Time of last update to record.

Class methods

classmethod df(include=None, join='inner', limit=100)

Convert to pd.DataFrame.

By default, shows all direct fields, except created_at.

If you’d like to include related fields, use parameter include.

Parameters:

  • include (str | list[str] | None, default: None) – Related fields to include as columns. Takes strings of form "labels__name", "cell_types__name", etc. or a list of such strings.

  • join (str, default: 'inner') – The join parameter of pandas.

Return type:

DataFrame

Examples

>>> labels = [ln.ULabel(name="Label {i}") for i in range(3)]
>>> ln.save(labels)
>>> ln.ULabel.filter().df(include=["created_by__name"])
classmethod filter(**expressions)

Query records.

Parameters:

expressions – Fields and values passed as Django query expressions.

Return type:

QuerySet

Returns:

A QuerySet.

See also

Examples

>>> ln.ULabel(name="my ulabel").save()
>>> ulabel = ln.ULabel.get(name="my ulabel")
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:

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
classmethod get(idlike=None, **expressions)

Get a single record.

Parameters:

  • idlike (int | str | None, default: None) – Either a uid stub, uid or an integer id.

  • expressions – Fields and values passed as Django query expressions.

Return type:

Record

Returns:

A record.

Raises:

lamindb.core.exceptions.DoesNotExist – In case no matching record is found.

See also

Examples

>>> ulabel = ln.ULabel.get("2riu039")
>>> ulabel = ln.ULabel.get(name="my-label")
classmethod lookup(field=None, return_field=None)

Return an auto-complete object for a field.

Parameters:

  • field (str | DeferredAttribute | None, default: None) – The field to look up the values for. Defaults to first string field.

  • return_field (str | DeferredAttribute | None, default: None) – The field to return. If None, returns the whole record.

Return type:

NamedTuple

Returns:

A NamedTuple of lookup information of the field values with a dictionary converter.

See also

search()

Examples

>>> import bionty as bt
>>> bt.settings.organism = "human"
>>> bt.Gene.from_source(symbol="ADGB-DT").save()
>>> lookup = bt.Gene.lookup()
>>> lookup.adgb_dt
>>> lookup_dict = lookup.dict()
>>> lookup_dict['ADGB-DT']
>>> lookup_by_ensembl_id = bt.Gene.lookup(field="ensembl_gene_id")
>>> genes.ensg00000002745
>>> lookup_return_symbols = bt.Gene.lookup(field="ensembl_gene_id", return_field="symbol")
classmethod search(string, *, field=None, limit=20, case_sensitive=False)

Search.

Parameters:

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

  • field (str | DeferredAttribute | None, default: None) – The field or fields to search. Search all string fields by default.

  • limit (int | None, default: 20) – Maximum amount of top results to return.

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

Return type:

QuerySet

Returns:

A sorted DataFrame of search results with a score in column score. If return_queryset is True. QuerySet.

See also

filter() lookup()

Examples

>>> ulabels = ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name")
>>> ln.save(ulabels)
>>> ln.ULabel.search("ULabel2")
classmethod using(instance)

Use a non-default LaminDB instance.

Parameters:

instance (str | None) – An instance identifier of form “account_handle/instance_name”.

Return type:

QuerySet

Examples

>>> ln.ULabel.using("account_handle/instance_name").search("ULabel7", field="name")
            uid    score
name
ULabel7  g7Hk9b2v  100.0
ULabel5  t4Jm6s0q   75.0
ULabel6  r2Xw8p1z   75.0

Methods

set_as_currently_used()

Set this record as the currently used source.

Examples

>>> record = bionty.Source.get(uid="...")
>>> record.set_as_currently_used()
delete()

Delete.

Return type:

None

save(*args, **kwargs)

Save.

Always saves to the default database.

Return type:

Record