ncbi_gene.ensembl_assemblies

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	ncbi_release	ncbi_assembly	ensembl_release	ensembl_assembly	compared_date
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10020	Dipodomys ordii Annotation Release 100	Dord_2.0	2020-03	Dord_2.0	2026-08-01
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10029	Cricetulus griseus Annotation Release 104	CriGri-PICRH-1.0	2023-01	CriGri-PICRH-1.0	2026-08-01
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10036	Mesocricetus auratus Annotation Release 103	BCM_Maur_2.0	2021-10	BCM_Maur_2.0	2026-08-06
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10047	Meriones unguiculatus Annotation Release 101	Bangor_MerUng_6.1	2023-11	Bangor_MerUng_6.1	2026-08-06
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	10089	Mus caroli Annotation Release 101	CAROLI_EIJ_v1.1	115	CAROLI_EIJ_v1.1	2020-07-15

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 6 of 7 columns)
   taxon_id | ncbi_release             | ncbi_assembly     | ensembl_release | ensembl_assembly  | compared_date
   -------- | ------------------------ | ----------------- | --------------- | ----------------- | -------------
0  10020    | Dipodomys ordii Annotat… | Dord_2.0          | 2020-03         | Dord_2.0          | 2026-08-01
1  10029    | Cricetulus griseus Anno… | CriGri-PICRH-1.0  | 2023-01         | CriGri-PICRH-1.0  | 2026-08-01
2  10036    | Mesocricetus auratus An… | BCM_Maur_2.0      | 2021-10         | BCM_Maur_2.0      | 2026-08-06
3  10047    | Meriones unguiculatus A… | Bangor_MerUng_6.1 | 2023-11         | Bangor_MerUng_6.1 | 2026-08-06
4  10089    | Mus caroli Annotation R… | CAROLI_EIJ_v1.1   | 115             | CAROLI_EIJ_v1.1   | 2020-07-15

Description

NCBI annotation releases and assemblies compared with Ensembl releases and assemblies, one row per taxon in the current comparison report.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for NCBI’s Ensembl assembly comparison report.
taxon_id	TEXT	NCBI taxonomy identifier for the compared species or strain.
ncbi_release	TEXT	NCBI annotation release included in the comparison.
ncbi_assembly	TEXT	NCBI assembly name included in the comparison.
ensembl_release	TEXT	Ensembl release included in the comparison.
ensembl_assembly	TEXT	Ensembl assembly name included in the comparison.
compared_date	DATE	Date NCBI compared the releases and assemblies.