bionty.Pathway#

class bionty.Pathway(name: str, ontology_id: Optional[str], abbr: Optional[str], synonyms: Optional[str], description: Optional[str], parents: List[Pathway], public_source: Optional[PublicSource])#
class bionty.Pathway(*db_args)

Bases: BioRegistry

Pathways - Gene Ontology, Pathway Ontology.

Notes

For more info, see tutorial Manage biological registries

Bulk create Pathway records via from_values.

Examples

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

Fields

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.

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 pathway records.

genes ManyToManyField

Genes that signifies the pathway.

feature_sets ManyToManyField

Featuresets linked to the pathway.

artifacts ManyToManyField

Artifacts linked to the pathway.

collections ManyToManyField

Collections linked to the pathway.

Methods