ncbi_gene.relationships

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	gene_id	relationship	related_taxon_id	related_gene_id
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10029	100689291	Related pseudogene	10029	100689484
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10029	100689337	Related functional gene	10029	100764163
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10029	100689484	Related functional gene	10029	100689291
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10029	100764163	Related pseudogene	10029	100689337
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10090	100008564	Related functional gene	10090	241627

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 5 of 6 columns)
   taxon_id | gene_id   | relationship            | related_taxon_id | related_gene_id
   -------- | --------- | ----------------------- | ---------------- | ---------------
0  10029    | 100689291 | Related pseudogene      | 10029            | 100689484
1  10029    | 100689337 | Related functional gene | 10029            | 100764163
2  10029    | 100689484 | Related functional gene | 10029            | 100689291
3  10029    | 100764163 | Related pseudogene      | 10029            | 100689337
4  10090    | 100008564 | Related functional gene | 10090            | 241627

Description

Selected NCBI Gene relationships, one row per directed pair of GeneIDs.

It includes readthrough, region, functional-gene, and pseudogene relationships, but is not a comprehensive relationship resource.

gene_id has the stated relationship to related_gene_id.

NCBI reports relationships symmetrically where appropriate, but the table retains its supplied row direction.

Orthologs are excluded; use orthologs when that table is available.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the NCBI Gene group file.
taxon_id	TEXT	NCBI taxonomy identifier for the source gene’s species or strain.
gene_id	TEXT	Source NCBI Gene identifier.
relationship	TEXT	NCBI relationship from gene_id to related_gene_id.
related_taxon_id	TEXT	NCBI taxonomy identifier for the related gene’s species or strain.
related_gene_id	TEXT	Related NCBI Gene identifier.