ncbi_gene.genes

Python
R

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

	sources	taxon_id	gene_id	gene_symbol	locus_tag	synonyms	db_xrefs	chromosome	map_location	description	gene_type	nomenclature_symbol	nomenclature_name	nomenclature_status	other_designations	modified_date	feature_types
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	7	5692769	NEWENTRY	None	[]	[]	None	None	Record to support submission of GeneRIFs for a...	other	None	None	None	[]	2024-11-13	[]
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	9	2827857	NEWENTRY	None	[]	[]	None	None	Record to support submission of GeneRIFs for a...	other	None	None	None	[]	2024-11-13	[]
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	11	10823747	NEWENTRY	None	[]	[]	None	None	Record to support submission of GeneRIFs for a...	other	None	None	None	[]	2024-11-01	[]
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	14	6951813	NEWENTRY	None	[]	[]	None	None	Record to support submission of GeneRIFs for a...	other	None	None	None	[]	2024-12-04	[]
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	19	3758873	NEWENTRY	None	[]	[]	None	None	Record to support submission of GeneRIFs for a...	other	None	None	None	[]	2024-12-04	[]

library(bedrockbio)

lf <- load_table("ncbi_gene.genes")
df <- head(lf, 5) |> collect()

head(df)

Sample output (5 rows, showing 8 of 17 columns)
   taxon_id | gene_id  | gene_symbol | locus_tag | chromosome | map_location | description              | gene_type
   -------- | -------- | ----------- | --------- | ---------- | ------------ | ------------------------ | ---------
0  7        | 5692769  | NEWENTRY    | —         | —          | —            | Record to support submi… | other
1  9        | 2827857  | NEWENTRY    | —         | —          | —            | Record to support submi… | other
2  11       | 10823747 | NEWENTRY    | —         | —          | —            | Record to support submi… | other
3  14       | 6951813  | NEWENTRY    | —         | —          | —            | Record to support submi… | other
4  19       | 3758873  | NEWENTRY    | —         | —          | —            | Record to support submi… | other

Description

Current NCBI Gene identity, nomenclature, and cross-reference records, one row per GeneID.

gene_symbol is NCBI’s default symbol and is not necessarily an HGNC symbol. synonyms are alternate symbols, while other_designations are alternate descriptive names. db_xrefs contains external database identifiers as db and normalized id pairs.

Partitions

Not partitioned.

Schema

Column	Type	Description
`sources`	`STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]`	Provenance for the NCBI Gene information file.
`taxon_id`	`TEXT`	NCBI taxonomy identifier for the species or strain associated with the gene.
`gene_id`	`TEXT`	Current stable numeric NCBI Gene identifier.
`gene_symbol`	`TEXT`	NCBI default gene symbol.
`locus_tag`	`TEXT`	NCBI locus tag, if supplied.
`synonyms`	`TEXT[]`	Alternative or unofficial gene symbols, with database-style prefixes removed.
`db_xrefs`	`STRUCT(db TEXT, id TEXT)[]`	External identifiers as `db` and normalized `id` pairs.
`chromosome`	`TEXT`	Chromosome on which NCBI places the gene, if supplied; mitochondrial genomes use MT.
`map_location`	`TEXT`	NCBI map location, if supplied.
`description`	`TEXT`	NCBI descriptive gene name, if supplied.
`gene_type`	`TEXT`	NCBI gene type.
`nomenclature_symbol`	`TEXT`	Symbol supplied by a nomenclature authority, if supplied.
`nomenclature_name`	`TEXT`	Full name supplied by a nomenclature authority, if supplied.
`nomenclature_status`	`TEXT`	Nomenclature authority status: O for official or I for interim, if supplied.
`other_designations`	`TEXT[]`	Alternate descriptive names assigned to the GeneID.
`modified_date`	`DATE`	Date NCBI last modified the gene record, if supplied.
`feature_types`	`TEXT[]`	Annotated feature types and classes or controlled vocabularies derived from selected RefSeq annotations.