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biodbs

NCBI

NCBI¶

Access gene and taxonomy data via the NCBI Datasets API.

Overview¶

NCBI provides:

Gene Data - Gene information and annotations
Taxonomy - Organism classification
Genome Assemblies - Reference genome data

Quick Start¶

from biodbs.fetch import (
    ncbi_get_gene,
    ncbi_symbol_to_id,
    ncbi_get_taxonomy,
)

# Get gene by Entrez ID
genes = ncbi_get_gene([7157, 672])

Gene Data¶

Get Genes¶

from biodbs.fetch import ncbi_get_gene

# By Entrez Gene ID
genes = ncbi_get_gene([7157, 672])

# Access gene data
for gene in genes.genes:
    print(f"{gene.gene_id}: {gene.symbol}")

Symbol to ID¶

from biodbs.fetch import ncbi_symbol_to_id

mapping = ncbi_symbol_to_id(["TP53", "BRCA1"])
# {'TP53': 7157, 'BRCA1': 672}

ID to Symbol¶

from biodbs.fetch import ncbi_id_to_symbol

mapping = ncbi_id_to_symbol([7157, 672])
# {7157: 'TP53', 672: 'BRCA1'}

Translate Gene IDs¶

from biodbs.fetch import ncbi_translate_gene_ids

result = ncbi_translate_gene_ids(
    ["TP53", "BRCA1"],
    from_type="symbol",
    to_type="entrez_id",
    taxon="human"
)

Taxonomy¶

from biodbs.fetch import ncbi_get_taxonomy

# By taxonomy ID
tax = ncbi_get_taxonomy([9606, 10090])

# Access taxonomy data
human = tax.get_taxon(9606)
print(human.organism_name)  # "Homo sapiens"

Using the Fetcher Class¶

from biodbs.fetch.NCBI import NCBI_Fetcher

fetcher = NCBI_Fetcher()
genes = fetcher.get_genes_by_id([7157, 672])

Ensembl - Alternative gene resource with genomic coordinates and VEP.
UniProt - Protein information for gene products.
ID Translation - Translate between Entrez Gene IDs and other identifiers using translate_gene_ids(..., database="ncbi").