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HGNC

Access authoritative human gene nomenclature via the HGNC REST API.

Overview

The HUGO Gene Nomenclature Committee (HGNC) is the authority for approved human gene symbols and names. biodbs provides:

  • Exact lookups by symbol, HGNC ID, Entrez ID, Ensembl ID, UniProt accession, or RefSeq accession
  • Wildcard search across any HGNC field
  • Cross-reference retrieval — get Ensembl, Entrez, UniProt IDs for any gene in one call

Quick Start

from biodbs.fetch import hgnc_fetch_by_symbol, hgnc_search_symbol

# Fetch a gene by symbol
data = hgnc_fetch_by_symbol("TP53")
entry = data[0]
print(entry.hgnc_id)         # "HGNC:11998"
print(entry.entrez_id)       # "7157"
print(entry.ensembl_gene_id) # "ENSG00000141510"

# Wildcard search
hits = hgnc_search_symbol("BRCA*")
print(hits.symbols())  # ['BRCA1', 'BRCA2', ...]

Fetch by Identifier

By Gene Symbol

from biodbs.fetch import hgnc_fetch_by_symbol

data = hgnc_fetch_by_symbol("EGFR")
entry = data[0]
print(entry.name)   # "epidermal growth factor receptor"
print(entry.locus_type)

By HGNC ID

from biodbs.fetch import hgnc_fetch_by_hgnc_id

data = hgnc_fetch_by_hgnc_id("HGNC:11998")
print(data[0].symbol)  # "TP53"

By Entrez Gene ID

from biodbs.fetch import hgnc_fetch_by_entrez_id

data = hgnc_fetch_by_entrez_id("7157")
print(data[0].symbol)  # "TP53"

By Ensembl Gene ID

from biodbs.fetch import hgnc_fetch_by_ensembl_id

data = hgnc_fetch_by_ensembl_id("ENSG00000141510")
print(data[0].symbol)  # "TP53"

By UniProt Accession

from biodbs.fetch import hgnc_fetch_by_uniprot_id

data = hgnc_fetch_by_uniprot_id("P04637")
print(data[0].symbol)  # "TP53"

By RefSeq Accession

from biodbs.fetch import hgnc_fetch_by_refseq

data = hgnc_fetch_by_refseq("NM_000546")
print(data[0].symbol)  # "TP53"

from biodbs.fetch import hgnc_search_symbol

# All ZNF family members
hits = hgnc_search_symbol("ZNF*")
print(len(hits))

# Single character wildcard
hits = hgnc_search_symbol("BRCA?")
print(hits.symbols())  # ['BRCA1', 'BRCA2']

from biodbs.fetch import hgnc_search

# Boolean / Solr query
hits = hgnc_search("status:Approved AND locus_group:non-coding+RNA")

# Field + term
hits = hgnc_search("locus_type", "RNA*")

Low-Level Fetch

from biodbs.fetch import hgnc_fetch

# Exact-match on any HGNC stored field
data = hgnc_fetch("alias_symbol", "p53")

Service Info

from biodbs.fetch import hgnc_info

info = hgnc_info()
print(info["response"]["numDoc"])          # total gene count
print(info["response"]["lastModified"])    # last DB update

Working with Results

data = hgnc_fetch_by_symbol("TP53")
entry = data[0]

# Key fields on HGNCEntry
entry.hgnc_id          # "HGNC:11998"
entry.symbol           # "TP53"
entry.name             # "tumor protein p53"
entry.locus_group      # "protein-coding gene"
entry.locus_type       # "gene with protein product"
entry.entrez_id        # "7157"
entry.ensembl_gene_id  # "ENSG00000141510"
entry.uniprot_ids      # ["P04637"]
entry.refseq_accession # ["NM_000546"]
entry.status           # "Approved"

# Convert to DataFrame
df = data.as_dataframe()

Using the Fetcher Class

from biodbs.fetch.HGNC import HGNC_Fetcher

fetcher = HGNC_Fetcher()
data = fetcher.fetch("symbol", "TP53")
data = fetcher.search("symbol", "TP53*")
  • ID Translation — HGNC powers the "hgnc" translation database in translate_gene_ids().
  • NCBI — Complementary gene information including gene summaries and genomic location.
  • UniProt — Fetch protein data for genes identified via HGNC.