ncbi_gene.accessions

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	gene_id	refseq_status	rna_accession	rna_geninfo_id	protein_accession	protein_geninfo_id	genomic_accession	genomic_geninfo_id	gene_start	gene_end	gene_is_forward_strand	assembly_name	mature_peptide_accession	mature_peptide_geninfo_id	gene_symbol
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	23	313740176	NA	None	None	NaN	NaN	NZ_CM184905.1	3367300669	9	124	False	None	None	None	rrf
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	23	313740177	NA	None	None	NaN	NaN	NZ_CM184905.1	3367300669	360	3253	False	None	None	None	AC55FV_RS00010
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	23	313740178	NA	None	None	NaN	NaN	NZ_CM184905.1	3367300669	3610	5152	False	None	None	None	AC55FV_RS00015
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	23	313740179	NA	None	None	WP_496980559.1	3367299665	NZ_CM184905.1	3367300669	5791	6384	False	None	None	None	AC55FV_RS00020
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	23	313740180	NaN	None	None	GIU33944.1	2038348879	BPFF01000243.1	2038348876	<NA>	<NA>	<NA>	None	None	None	nrfF

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 17 columns)
   taxon_id | gene_id   | refseq_status | rna_accession | rna_geninfo_id | protein_accession | protein_geninfo_id | genomic_accession
   -------- | --------- | ------------- | ------------- | -------------- | ----------------- | ------------------ | -----------------
0  23       | 313740176 | NA            | —             | —              | —                 | —                  | NZ_CM184905.1
1  23       | 313740177 | NA            | —             | —              | —                 | —                  | NZ_CM184905.1
2  23       | 313740178 | NA            | —             | —              | —                 | —                  | NZ_CM184905.1
3  23       | 313740179 | NA            | —             | —              | WP_496980559.1    | 3367299665         | NZ_CM184905.1
4  23       | 313740180 | —             | —             | —              | GIU33944.1        | 2038348879         | BPFF01000243.1

Description

NCBI Gene mappings to genomic, RNA, protein, and mature-peptide sequence accessions.

One row describes a supplied set of accessions and genomic placement; it can include international-sequence, Swiss-Prot, and RefSeq records.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the NCBI Gene accession mapping file.
taxon_id	TEXT	NCBI taxonomy identifier for the gene’s species or strain.
gene_id	TEXT	NCBI Gene identifier.
refseq_status	TEXT	RefSeq record status — INFERRED, MODEL, NA, PREDICTED, PROVISIONAL, REVIEWED, SUPPRESSED, or VALIDATED — when the row contains RefSeq data; null for non-RefSeq records.
rna_accession	TEXT	Versioned RNA nucleotide accession, if supplied.
rna_geninfo_id	TEXT	Legacy NCBI GenInfo identifier for the RNA accession, if supplied.
protein_accession	TEXT	Versioned protein accession, if supplied.
protein_geninfo_id	TEXT	Legacy NCBI GenInfo identifier for the protein accession, if supplied.
genomic_accession	TEXT	Versioned genomic nucleotide accession, if supplied.
genomic_geninfo_id	TEXT	Legacy NCBI GenInfo identifier for the genomic accession, if supplied.
gene_start	BIGINT	One-based inclusive genomic gene start position, if supplied.
gene_end	BIGINT	One-based inclusive genomic gene end position, if supplied.
gene_is_forward_strand	BOOLEAN	Whether the gene is on the forward strand — true for source +, false for source -, and null for source ? when orientation is not applicable.
assembly_name	TEXT	NCBI assembly name for the genomic placement, if supplied.
mature_peptide_accession	TEXT	Versioned mature peptide accession, if supplied.
mature_peptide_geninfo_id	TEXT	Legacy NCBI GenInfo identifier for the mature peptide accession, if supplied.
gene_symbol	TEXT	NCBI default gene symbol, if supplied.