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.

is_locked: bool¶: Whether the record is locked for edits.

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

See also

Guide: Query & search registries
Django documentation: Queries

Examples

>>> ln.Project(name="my label").save()
>>> ln.Project.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

record = ln.Record.get("FvtpPJLJ")
record = ln.Record.get(name="my-label")

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

Evaluate and convert to pd.DataFrame.

By default, maps simple fields and foreign keys onto DataFrame columns.

Guide: Query & search registries

Parameters:

include (str | list[str] | None, default: None) – Related data to include as columns. Takes strings of form "records__name", "cell_types__name", etc. or a list of such strings. For Artifact, Record, and Run, can also pass "features" to include features with data types pointing to entities in the core schema. If "privates", includes private fields (fields starting with _).
features (bool | list[str], default: False) – Configure the features to include. Can be a feature name or a list of such names. If "queryset", infers the features used within the current queryset. Only available for Artifact, Record, and Run.
limit (int, default: 100) – Maximum number of rows to display. If None, includes all results.
order_by – Field name to order the records by. Prefix with ‘-’ for descending order. Defaults to ‘-id’ to get the most recent records. This argument is ignored if the queryset is already ordered or if the specified field does not exist.

Return type:

DataFrame

Examples

Include the name of the creator:

ln.Record.to_dataframe(include="created_by__name"])

Include features:

ln.Artifact.to_dataframe(include="features")

Include selected features:

ln.Artifact.to_dataframe(features=["cell_type_by_expert", "cell_type_by_model"])

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

records = ln.Record.from_values(["Label1", "Label2", "Label3"], field="name").save()
ln.Record.search("Label2")

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

Lookup via auto-complete on .:

import bionty as bt
bt.Gene.from_source(symbol="ADGB-DT").save()
lookup = bt.Gene.lookup()
lookup.adgb_dt

Look up via auto-complete in dictionary:

lookup_dict = lookup.dict()
lookup_dict['ADGB-DT']

Look up via a specific field:

lookup_by_ensembl_id = bt.Gene.lookup(field="ensembl_gene_id")
genes.ensg00000002745

Return a specific field value instead of the full record:

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.Record.using("account_handle/instance_name").search("label7", field="name")

Methods¶

save(*args, **kwargs)¶

Save the source record.

Return type:: Source

restore()¶

Restore from trash onto the main branch.

Return type:: None

delete(permanent=None, **kwargs)¶

Delete record.

Parameters:: permanent (bool | None, default: None) – Whether to permanently delete the record (skips trash). If None, performs soft delete if the record is not already in the trash.
Return type:: None

Examples

For any SQLRecord object record, call:

>>> record.delete()