bionty.Gene

class bionty.Gene(symbol: str | None, stable_id: str | None, ensembl_gene_id: str | None, ncbi_gene_ids: str | None, biotype: str | None, description: str | None, synonyms: str | None, organism: lnschema_bionty.models.Organism | None, public_source: lnschema_bionty.models.PublicSource | None)

class bionty.Gene(*db_args)

Bases: BioRegistry

Genes - Ensembl, NCBI Gene.

Notes

Bulk create Gene records via from_values.

Examples

>>> record = bionty.Gene.from_public(symbol="TCF7", organism="human")

Fields

id AutoField

Internal id, valid only in one DB instance.

uid CharField

A universal id (hash of selected field).

symbol CharField

A unique short form of gene name.

stable_id CharField

Stable ID of a gene that doesn’t have ensembl_gene_id, e.g. a yeast gene.

ensembl_gene_id CharField

Ensembl gene stable ID, in the form ENS[organism prefix][feature type prefix][a unique eleven digit number].

ncbi_gene_ids TextField

Bar-separated (|) NCBI Gene IDs that correspond to this Ensembl Gene ID. NCBI Gene ID, also known as Entrez Gene ID, in the form of numeric string, 1 to 9 digits.

biotype CharField

Type of the gene.

description TextField

Description of the gene.

synonyms TextField

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

organism ForeignKey

Organism this gene associates with.

public_source ForeignKey

PublicSource this gene 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.

artifacts ManyToManyField

Artifacts linked to the gene.

collections ManyToManyField

Collections linked to the gene.

feature_sets ManyToManyField

Featuresets linked to this gene.

Methods