ncbi_gene.ensembl_relationships

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	gene_id	ensembl_gene_id	transcript_accession	ensembl_transcript_id	protein_accession	ensembl_protein_id
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10020	105980080	ENSDORG00000010179	XM_013009162.1	ENSDORT00000010179.2	XP_012864616.1	ENSDORP00000009570.2
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10020	105980082	ENSDORG00000005965	XM_013008781.1	ENSDORT00000028579.1	XP_012864235.1	ENSDORP00000023316.1
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10020	105980083	ENSDORG00000000951	XM_013008783.1	ENSDORT00000000951.2	XP_012864237.1	ENSDORP00000000892.2
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10020	105980084	ENSDORG00000002802	XM_013008787.1	ENSDORT00000002802.2	XP_012864241.1	ENSDORP00000002632.2
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10020	105980085	ENSDORG00000024341	XM_013008785.1	ENSDORT00000026093.1	XP_012864239.1	ENSDORP00000018520.1

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 7 of 8 columns)
   taxon_id | gene_id   | ensembl_gene_id    | transcript_accession | ensembl_transcript_id | protein_accession | ensembl_protein_id
   -------- | --------- | ------------------ | -------------------- | --------------------- | ----------------- | --------------------
0  10020    | 105980080 | ENSDORG00000010179 | XM_013009162.1       | ENSDORT00000010179.2  | XP_012864616.1    | ENSDORP00000009570.2
1  10020    | 105980082 | ENSDORG00000005965 | XM_013008781.1       | ENSDORT00000028579.1  | XP_012864235.1    | ENSDORP00000023316.1
2  10020    | 105980083 | ENSDORG00000000951 | XM_013008783.1       | ENSDORT00000000951.2  | XP_012864237.1    | ENSDORP00000000892.2
3  10020    | 105980084 | ENSDORG00000002802 | XM_013008787.1       | ENSDORT00000002802.2  | XP_012864241.1    | ENSDORP00000002632.2
4  10020    | 105980085 | ENSDORG00000024341 | XM_013008785.1       | ENSDORT00000026093.1  | XP_012864239.1    | ENSDORP00000018520.1

Description

NCBI’s best RefSeq-to-Ensembl RNA and protein feature matches, one row per reported match.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the NCBI Gene Ensembl mapping file.
taxon_id	TEXT	NCBI taxonomy identifier for the gene’s species or strain.
gene_id	TEXT	NCBI Gene identifier.
ensembl_gene_id	TEXT	Matched Ensembl gene identifier.
transcript_accession	TEXT	Versioned matching RefSeq transcript accession, if supplied.
ensembl_transcript_id	TEXT	Matched Ensembl transcript identifier, if supplied.
protein_accession	TEXT	Versioned matching RefSeq protein accession, if supplied.
ensembl_protein_id	TEXT	Matched Ensembl protein identifier, if supplied.