ncbi_gene.refseq_uniprot_mapping

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	refseq_accession	uniprot_accession	refseq_taxon_id	uniprot_taxon_id	method
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	AP_000002.1	A0A9W3HR73	114424	114429	identical
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	AP_000003.1	A0A9W3HR54	114424	114429	identical
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	AP_000004.1	A0A9W3N270	114424	114429	identical
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	AP_000010.1	Q96624	114424	114429	identical
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	AP_000011.1	Q96625	114424	114429	similar

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 5 of 6 columns)
   refseq_accession | uniprot_accession | refseq_taxon_id | uniprot_taxon_id | method
   ---------------- | ----------------- | --------------- | ---------------- | ---------
0  AP_000002.1      | A0A9W3HR73        | 114424          | 114429           | identical
1  AP_000003.1      | A0A9W3HR54        | 114424          | 114429           | identical
2  AP_000004.1      | A0A9W3N270        | 114424          | 114429           | identical
3  AP_000010.1      | Q96624            | 114424          | 114429           | identical
4  AP_000011.1      | Q96625            | 114424          | 114429           | similar

Description

NCBI RefSeq protein to UniProtKB protein mappings, one row per reported accession pair.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the NCBI RefSeq–UniProtKB collaboration file.
refseq_accession	TEXT	RefSeq protein accession.
uniprot_accession	TEXT	Corresponding UniProt protein accession.
refseq_taxon_id	TEXT	NCBI taxonomy identifier for the RefSeq protein.
uniprot_taxon_id	TEXT	NCBI taxonomy identifier for the UniProt protein; it can differ from refseq_taxon_id.
method	TEXT	Source-assigned mapping method — uniprot for a mapping imported from UniProt, identical for an identical protein sequence and assigned organism, or similar for the same assigned organism with >90% identity over >80% coverage.