ncbi_gene.history

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	gene_id	discontinued_gene_id	discontinued_symbol	discontinued_date
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	1000373	None	80521939	RdRp	2023-05-06
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	1000585	None	33310776	NEWENTRY	2023-06-16
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	1000685	None	12216884	C1	2012-12-28
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	1000685	None	12284404	NEWENTRY	2026-09-02
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	1000686	None	12216891	C1	2012-12-27

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 5 of 6 columns)
   taxon_id | gene_id | discontinued_gene_id | discontinued_symbol | discontinued_date
   -------- | ------- | -------------------- | ------------------- | -----------------
0  1000373  | —       | 80521939             | RdRp                | 2023-05-06
1  1000585  | —       | 33310776             | NEWENTRY            | 2023-06-16
2  1000685  | —       | 12216884             | C1                  | 2012-12-28
3  1000685  | —       | 12284404             | NEWENTRY            | 2026-09-02
4  1000686  | —       | 12216891             | C1                  | 2012-12-27

Description

NCBI Gene records for discontinued GeneIDs, one row per discontinued GeneID.

gene_id is the current replacement GeneID when NCBI provides one; it is null when the discontinued record has no replacement.

Use this table to resolve older GeneIDs before querying current NCBI Gene tables.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the NCBI Gene history file.
taxon_id	TEXT	NCBI taxonomy identifier for the species or strain associated with the discontinued gene.
gene_id	TEXT	Current replacement NCBI Gene identifier, if NCBI provides one.
discontinued_gene_id	TEXT	Discontinued NCBI Gene identifier.
discontinued_symbol	TEXT	Symbol assigned to the discontinued GeneID, if supplied.
discontinued_date	DATE	Date NCBI discontinued or replaced the GeneID.