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: SQLRecord, 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 (base62-encoded hash of defining fields).

entity: str¶: Entity class name with schema, e.g. bionty.CellType.

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 been 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.

Relational fields¶

branch: Branch¶: Whether record is on a branch or in another “special state”.

space: Space¶: The space in which the record lives.

created_by: User¶: Creator of record.

run: Run | None¶: Run that created record.

dataframe_artifact: Artifact¶: Dataframe artifact that corresponds to this source.

artifacts: Artifact¶: Additional files that correspond to this source.

Class methods¶

classmethod filter(*queries, **expressions)¶

Query records.

Parameters:

queries – One or multiple Q objects.
expressions – Fields and values passed as Django query expressions.

Return type:

QuerySet

Returns:

A QuerySet.

See also

Guide: Query & search registries
Django documentation: Queries

Examples

>>> ln.ULabel(name="my label").save()
>>> ln.ULabel.filter(name__startswith="my").to_dataframe()

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.

Raises:

lamindb.errors.DoesNotExist – In case no matching record is found.

Return type:

SQLRecord

See also

Guide: Query & search registries
Django documentation: Queries

Examples

ulabel = ln.ULabel.get("FvtpPJLJ")
ulabel = ln.ULabel.get(name="my-label")

classmethod df(include=None, features=False, limit=100)¶

None

Return type:: DataFrame

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 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.
keep – When multiple records are found for a lookup, how to return the records. - "first": return the first record. - "last": return the last record. - False: return all records.

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 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¶

save(*args, **kwargs)¶

Save the source record.

Return type:: Source

delete(permanent=None, **kwargs)¶

Delete record.

Parameters:: permanent (bool | None, default: None) – Whether to permanently delete the record (skips trash).
Return type:: None

Examples

For any SQLRecord object record, call:

>>> record.delete()