ncbi_gene.orthologs

Python
R

import bedrock_bio as bb

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

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

	sources	taxon_id	gene_id	ortholog_taxon_id	ortholog_gene_id
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10090	100042165	10029	100755241
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10090	100042165	10036	101830611
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10090	100042165	10041	114691792
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10090	100042165	10047	110562826
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10090	100042165	10089	110294739

library(bedrockbio)

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

head(df)

Sample output (5 rows, showing 4 of 5 columns)
   taxon_id | gene_id   | ortholog_taxon_id | ortholog_gene_id
   -------- | --------- | ----------------- | ----------------
0  10090    | 100042165 | 10029             | 100755241
1  10090    | 100042165 | 10036             | 101830611
2  10090    | 100042165 | 10041             | 114691792
3  10090    | 100042165 | 10047             | 110562826
4  10090    | 100042165 | 10089             | 110294739

Description

Directed NCBI Gene orthology pairs, one row per primary GeneID and ortholog GeneID pair.

NCBI does not report the pairs symmetrically: gene_id is the primary member chosen for an ortholog set, while ortholog_gene_id is another member.

The source’s constant relationship value of Ortholog is omitted.

Partitions

Not partitioned.

Schema

Column	Type	Description
`sources`	`STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]`	Provenance for the NCBI Gene orthologs file.
`taxon_id`	`TEXT`	NCBI taxonomy identifier for the primary gene’s species or strain.
`gene_id`	`TEXT`	Primary NCBI Gene identifier in the ortholog set.
`ortholog_taxon_id`	`TEXT`	NCBI taxonomy identifier for the ortholog gene’s species or strain.
`ortholog_gene_id`	`TEXT`	NCBI Gene identifier for the orthologous gene.