lnschema_bionty.Gene

class lnschema_bionty.Gene(symbol: Optional[str], stable_id: Optional[str], ensembl_gene_id: Optional[str], ncbi_gene_ids: Optional[str], biotype: Optional[str], description: Optional[str], synonyms: Optional[str], species: Optional[Species], bionty_source: Optional[BiontySource])

class lnschema_bionty.Gene(*db_args)

Bases: BioRegistry

Genes - Ensembl, NCBI Gene.

Notes

Bulk create Gene records via from_values.

Examples

>>> record = lb.Gene.from_bionty(symbol="TCF7", species="human")
>>> record.save()

Fields

id CharField

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

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[species 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.

species ForeignKey

Species this gene associates with.

bionty_source ForeignKey

BiontySource 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.

files ManyToManyField

Files linked to the gene.

datasets ManyToManyField

Datasets linked to the gene.

feature_sets ManyToManyField

Featuresets linked to this gene.

Methods