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: Organism | None, public_source: PublicSource | None)

Bases: BioRegistry, TracksRun, TracksUpdates

Genes - Ensembl, NCBI Gene.

Notes

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

Bulk create Gene records via from_values.

Examples

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

Fields

run: Run

Last run that created or updated the record.

id

Internal id, valid only in one DB instance.

uid

A universal id (hash of selected field).

symbol

A unique short form of gene name.

stable_id

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

ensembl_gene_id

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

ncbi_gene_ids

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

Type of the gene.

description

Description of the gene.

synonyms

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

organism

Organism this gene associates with.

public_source

PublicSource this gene associates with.

previous_runs: Run

Sequence of runs that created or updated the record.

artifacts

Artifacts linked to the gene.

feature_sets

Featuresets linked to this gene.

created_at: datetime

Time of creation of record.

created_by: User

Creator of record.

updated_at: datetime

Time of last update to record.

Methods