ensembl.species

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('ensembl.species')

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

Out[1]:

	sources	release	ensembl_division	ensembl_collection	species_name	taxon_id	scientific_name	common_name	assembly_name	genbank_assembly_accession
0	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	bacteria	bacteria_126_collection	acinetobacter_baumannii_gca_000805365	470	Acinetobacter baumannii gca 000805365	Acinetobacter baumannii str. 1 (GCA_000805365)	ASM80536v1	GCA_000805365.1
1	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	bacteria	bacteria_0_collection	bacillus_subtilis_subsp_subtilis_str_168_gca_0...	224308	Bacillus subtilis subsp subtilis str 168 gca 0...	Bacillus subtilis subsp. subtilis str. 168 (GC...	ASM904v1	GCA_000009045.1
2	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	bacteria	bacteria_125_collection	bacteroides_fragilis_nctc_9343_gca_000025985	272559	Bacteroides fragilis nctc 9343 gca 000025985	Bacteroides fragilis NCTC 9343 str. ATCC 25285...	ASM2598v1	GCA_000025985.1
3	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	bacteria	bacteria_0_collection	bacteroides_thetaiotaomicron_vpi_5482_gca_0000...	226186	Bacteroides thetaiotaomicron vpi 5482 gca 0000...	Bacteroides thetaiotaomicron VPI-5482 (GCA_000...	ASM1106v1	GCA_000011065.1
4	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	bacteria	bacteria_68_collection	bordetella_pertussis_18323_gca_000306945	568706	Bordetella pertussis 18323 gca 000306945	Bordetella pertussis 18323 (GCA_000306945)	ASM30694v1	GCA_000306945.1

R

In [1]:

library(bedrockbio)

lf <- load_table("ensembl.species")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 10 columns)
   release | ensembl_division | ensembl_collection      | species_name             | taxon_id | scientific_name          | common_name              | assembly_name
   ------- | ---------------- | ----------------------- | ------------------------ | -------- | ------------------------ | ------------------------ | -------------
0  63      | bacteria         | bacteria_126_collection | acinetobacter_baumannii… | 470      | Acinetobacter baumannii… | Acinetobacter baumannii… | ASM80536v1
1  63      | bacteria         | bacteria_0_collection   | bacillus_subtilis_subsp… | 224308   | Bacillus subtilis subsp… | Bacillus subtilis subsp… | ASM904v1
2  63      | bacteria         | bacteria_125_collection | bacteroides_fragilis_nc… | 272559   | Bacteroides fragilis nc… | Bacteroides fragilis NC… | ASM2598v1
3  63      | bacteria         | bacteria_0_collection   | bacteroides_thetaiotaom… | 226186   | Bacteroides thetaiotaom… | Bacteroides thetaiotaom… | ASM1106v1
4  63      | bacteria         | bacteria_68_collection  | bordetella_pertussis_18… | 568706   | Bordetella pertussis 18… | Bordetella pertussis 18… | ASM30694v1

Description

Selected Ensembl and Ensembl Genomes species and genome assemblies.

The independently released Ensembl collections and their release numbers identify the source for each row.

One row per selected assembly.

Use genbank_assembly_accession to select its downstream annotation partitions.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the release species file.
release	TEXT	Ensembl or Ensembl Genomes release number for this row.
ensembl_division	TEXT	Ensembl publishing division: vertebrates, bacteria, fungi, metazoa, plants, or protists.
ensembl_collection	TEXT	Ensembl Genomes collection directory for bacterial species, if applicable.
species_name	TEXT	Ensembl’s lowercase, underscore-separated species key (e.g. homo_sapiens).
taxon_id	TEXT	NCBI taxonomy ID for the species (e.g. 9606 for human).
scientific_name	TEXT	Binomial scientific name (e.g. Homo sapiens).
common_name	TEXT	Common name of the species (e.g. human). May be null.
assembly_name	TEXT	Reference genome assembly name (e.g. GRCh38).
genbank_assembly_accession	TEXT	GenBank assembly accession (e.g. GCA_000001405.29). May be null.