lnschema_bionty.Protein

class lnschema_bionty.Protein(name: Optional[str], uniprotkb_id: Optional[str], synonyms: Optional[str], length: Optional[int], gene_symbol: Optional[str], ensembl_gene_ids: Optional[str], species: Optional[Species], bionty_source: Optional[BiontySource])

class lnschema_bionty.Protein(*db_args)

Bases: BioRegistry

Proteins - Uniprot.

Notes

Bulk create Protein records via from_values.

Examples

>>> record = lb.Protein.from_bionty(name="Synaptotagmin-15B", species="human")
✅ validated 1 Protein record from Bionty on name: Synaptotagmin-15B
>>> record
Protein(id=KiCrq9BBTviZ, name=Synaptotagmin-15B, uniprotkb_id=X6R8R1, synonyms=, length=474, gene_symbol=SYT15B, species_id=uHJU, bionty_source_id=SFni, created_by_id=DzTjkKse) # noqa

>>> record = lb.Protein.from_bionty(gene_symbol="SYT15B", species="human")
✅ validated 1 Protein record from Bionty on gene_symbol: SYT15B
>>> record
Protein(id=KiCrq9BBTviZ, name=Synaptotagmin-15B, uniprotkb_id=X6R8R1, synonyms=, length=474, gene_symbol=SYT15B, species_id=uHJU, bionty_source_id=SFni, created_by_id=DzTjkKse) # noqa
>>> 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.

name CharField

Unique name of a protein.

uniprotkb_id CharField

UniProt protein ID, 6 alphanumeric characters, possibly suffixed by 4 more.

synonyms TextField

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

length BigIntegerField

Length of the protein sequence.

gene_symbol CharField

The primary gene symbol corresponds to this protein.

ensembl_gene_ids TextField

Bar-separated (|) Ensembl Gene IDs that correspond to this protein.

species ForeignKey

Species this protein associates with.

bionty_source ForeignKey

BiontySource this protein 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 protein.

datasets ManyToManyField

Datasets linked to the protein.

feature_sets ManyToManyField

Featuresets linked to this protein.

Methods