ncbi_gene.summaries

Python
R

import bedrock_bio as bb

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

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

	sources	taxon_id	gene_id	summary_source	summary
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100188	138614750	RefSeq	This record represents a tRNA model predicted ...
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100188	138615018	RefSeq	This record represents a tRNA model predicted ...
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100188	138615019	RefSeq	This record represents a tRNA model predicted ...
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100188	138615116	RefSeq	This record represents a tRNA model predicted ...
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100188	138615289	RefSeq	This record represents a tRNA model predicted ...

library(bedrockbio)

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

head(df)

Sample output (5 rows, showing 4 of 5 columns)
   taxon_id | gene_id   | summary_source | summary
   -------- | --------- | -------------- | ------------------------
0  100188   | 138614750 | RefSeq         | This record represents …
1  100188   | 138615018 | RefSeq         | This record represents …
2  100188   | 138615019 | RefSeq         | This record represents …
3  100188   | 138615116 | RefSeq         | This record represents …
4  100188   | 138615289 | RefSeq         | This record represents …

Description

Current NCBI summary text for live genes that have a summary, one row per NCBI GeneID.

summary_source identifies the provider of the summary text when NCBI supplies one.

Gene IDs are globally stable NCBI identifiers; taxon_id identifies the organism or strain.

Partitions

Not partitioned.

Schema

Column	Type	Description
`sources`	`STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]`	Provenance for the NCBI Gene summary file.
`taxon_id`	`TEXT`	NCBI taxonomy identifier for the species or strain associated with the gene.
`gene_id`	`TEXT`	Current stable numeric NCBI Gene identifier.
`summary_source`	`TEXT`	Provider of the summary text, when NCBI supplies one.
`summary`	`TEXT`	NCBI gene summary text.