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bedrock.bio

hgnc.genes

import bedrock_bio as bb

rel = bb.load_table('hgnc.genes')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources hgnc_id symbol name locus_group locus_type status cytogenetic_location alias_symbols alias_names ... cd_symbol lncrnadb_id enzyme_ec_accessions intermediate_filament_db_id rna_central_id lncipedia_symbol gtrnadb_id agr_id mane_select_transcript gencc_id
0 [{'url': 'https://storage.googleapis.com/publi... HGNC:100 ASIC1 acid sensing ion channel subunit 1 protein-coding gene gene with protein product Approved 12q13.12 [BNaC2, hBNaC2] [] ... None None [] None None None None HGNC:100 {'ensembl_transcript_id': 'ENST00000447966.7',... NaN
1 [{'url': 'https://storage.googleapis.com/publi... HGNC:10000 RGS4 regulator of G protein signaling 4 protein-coding gene gene with protein product Approved 1q23.3 [] [] ... None None [] None None None None HGNC:10000 {'ensembl_transcript_id': 'ENST00000367909.11'... NaN
2 [{'url': 'https://storage.googleapis.com/publi... HGNC:10001 RGS5 regulator of G protein signaling 5 protein-coding gene gene with protein product Approved 1q23.3 [] [] ... None None [] None None None None HGNC:10001 {'ensembl_transcript_id': 'ENST00000313961.10'... HGNC:10001
3 [{'url': 'https://storage.googleapis.com/publi... HGNC:10002 RGS6 regulator of G protein signaling 6 protein-coding gene gene with protein product Approved 14q24.2 [] [] ... None None [] None None None None HGNC:10002 {'ensembl_transcript_id': 'ENST00000553525.6',... HGNC:10002
4 [{'url': 'https://storage.googleapis.com/publi... HGNC:10003 RGS7 regulator of G protein signaling 7 protein-coding gene gene with protein product Approved 1q43 [] [] ... None None [] None None None None HGNC:10003 {'ensembl_transcript_id': 'ENST00000440928.6',... HGNC:10003

Description

Section titled “Description”

HGNC gene symbol reports, one row per stable HGNC identifier.

symbol is HGNC’s approved symbol. alias_symbols and previous_symbols resolve historical or alternate symbols; hgnc_id identifies the matched report. withdrawn covers symbols that HGNC has withdrawn or merged/split into other reports.

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Provenance for the HGNC complete-set file.
hgnc_id TEXT Stable HGNC identifier, such as HGNC:11998.
symbol TEXT HGNC’s current approved gene symbol.
name TEXT HGNC’s current approved gene name.
locus_group TEXT HGNC locus group, such as protein-coding gene or non-coding RNA.
locus_type TEXT HGNC locus type within locus_group.
status TEXT HGNC report status. The current complete-set file supplies Approved records.
cytogenetic_location TEXT HGNC cytogenetic location, if supplied.
alias_symbols TEXT[] Other symbols HGNC recognizes for the gene.
alias_names TEXT[] Other names HGNC recognizes for the gene.
previous_symbols TEXT[] Symbols that were previously HGNC-approved for the gene.
previous_names TEXT[] Names that were previously HGNC-approved for the gene.
family_names TEXT[] HGNC gene-family names associated with the gene. HGNC calls this source field gene_group.
family_ids TEXT[] HGNC gene-family identifiers associated with the gene. HGNC calls this source field gene_group_id.
approved_at DATE Date HGNC first approved or reserved the record, if supplied.
symbol_changed_at DATE Date HGNC last changed the approved symbol, if supplied.
name_changed_at DATE Date HGNC last changed the approved name, if supplied.
modified_at DATE Date HGNC last modified the record, if supplied.
ncbi_gene_id TEXT Linked NCBI Gene identifier, if supplied; joins registry.genes.
ensembl_gene_id TEXT Linked Ensembl human gene identifier, if supplied; joins ensembl.genes for GRCh38.p14.
vega_gene_id TEXT Linked legacy Vega gene identifier, if supplied.
ucsc_id TEXT Linked UCSC gene identifier, if supplied.
ena_accessions TEXT[] INSDC accession numbers, including GenBank, ENA, and DDBJ; empty when HGNC does not supply one.
refseq_accessions TEXT[] RefSeq nucleotide accession numbers; empty when HGNC does not supply one.
ccds_ids TEXT[] Consensus CDS identifiers; empty when HGNC does not supply one.
uniprot_accessions TEXT[] UniProt protein accession numbers; empty when HGNC does not supply one.
pubmed_ids TEXT[] PubMed or Europe PMC identifiers; empty when HGNC does not supply one.
mgd_ids TEXT[] Mouse Genome Informatics database identifiers; empty when HGNC does not supply one.
rgd_ids TEXT[] Rat Genome Database gene identifiers; empty when HGNC does not supply one.
lsdbs STRUCT(name TEXT, url TEXT)[] Locus-specific database mappings with name and url fields; empty when HGNC does not supply one.
cosmic_symbol TEXT COSMIC gene symbol, if supplied. HGNC notes that COSMIC is no longer updated.
omim_ids TEXT[] OMIM identifiers; empty when HGNC does not supply one.
mirbase_id TEXT miRBase identifier, if supplied.
homeodb_id TEXT Homeobox Database identifier, if supplied.
snornabase_id TEXT snoRNABase identifier, if supplied.
bioparadigms_slc_symbol TEXT Bioparadigms SLC database symbol, if supplied.
orphanet_id TEXT Orphanet identifier, if supplied.
pseudogene_dot_org_id TEXT Pseudogene.org identifier, if supplied.
horde_symbol TEXT HORDE gene symbol, if supplied.
merops_id TEXT MEROPS peptidase identifier, if supplied.
imgt_symbol TEXT IMGT gene symbol, if supplied.
iuphar_object_id TEXT Numeric IUPHAR/BPS Guide to Pharmacology object identifier, if supplied.
kznf_gene_catalog TEXT KZNF Gene Catalog identifier, if supplied.
mamit_trnadb_id TEXT Mamit-tRNA database identifier, if supplied.
cd_symbol TEXT Human Cell Differentiation Molecule database symbol, if supplied.
lncrnadb_id TEXT lncRNA Database identifier, if supplied. HGNC notes that this resource is defunct.
enzyme_ec_accessions TEXT[] ENZYME EC accession numbers; empty when HGNC does not supply one.
intermediate_filament_db_id TEXT Human Intermediate Filament Database identifier, if supplied.
rna_central_id TEXT RNAcentral identifier, if supplied.
lncipedia_symbol TEXT LNCipedia gene symbol, if supplied.
gtrnadb_id TEXT GtRNAdb identifier, if supplied.
agr_id TEXT Alliance of Genome Resources HGNC identifier, if supplied.
mane_select_transcript STRUCT(ensembl_transcript_id TEXT, refseq_transcript_accession TEXT) Matched MANE Select transcript with Ensembl and RefSeq identifiers, if supplied.
gencc_id TEXT GenCC HGNC identifier, if supplied.