bionty.Pathway

class bionty.Pathway(name: str, ontology_id: str | None, abbr: str | None, synonyms: str | None, description: str | None, parents: list[Pathway], public_source: PublicSource | None)

Bases: BioRegistry, TracksRun, TracksUpdates

Pathways - Gene Ontology, Pathway Ontology.

Notes

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

Bulk create Pathway records via from_values.

Examples

>>> record = bionty.Pathway.from_public(ontology_id="GO:1903353")
>>> record.save()

Fields

run ForeignKey

Last run that created or updated the record. Run

id AutoField

Internal id, valid only in one DB instance.

uid CharField

A universal id (hash of selected field).

name CharField

Name of the pathway.

ontology_id CharField

Ontology ID of the pathway.

abbr CharField

A unique abbreviation of pathway.

synonyms TextField

Bar-separated (|) synonyms that correspond to this pathway.

description TextField

Description of the pathway.

public_source ForeignKey

PublicSource this pathway associates with.

previous_runs ManyToManyField

Sequence of runs that created or updated the record.

parents ManyToManyField

Parent pathway records.

genes ManyToManyField

Genes that signifies the pathway.

feature_sets ManyToManyField

Featuresets linked to the pathway.

artifacts ManyToManyField

Artifacts linked to the pathway.

created_at DateTimeField

Time of creation of record.

created_by ForeignKey

Creator of record. User

updated_at DateTimeField

Time of last update to record.

Methods