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eskapee

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assembly
large_stringclasses
6 values
sequence_id
int64
0
13
taxon
int64
470
1.13M
taxon_name
large_stringclasses
6 values
taxon_short
large_stringclasses
6 values
contig
large_stringlengths
11
13
seq_len
int64
1.31k
6.26M
description
large_stringlengths
44
81
strand
large_stringclasses
1 value
sequence
large_stringlengths
1.31k
6.26M
GCF_000005845.2
0
511,145
Escherichia coli
E. coli MG1655
NC_000913.3
4,641,652
Escherichia coli str. K-12 substr. MG1655, complete genome
forward
"AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAA(...TRUNCATED)
GCF_000006765.1
4
208,964
Pseudomonas aeruginosa
P. aeruginosa
NC_002516.2
6,264,404
Pseudomonas aeruginosa PAO1, complete genome
forward
"TTTAAAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATAGATACAAGGAAGTCATTTTTCTTTTA(...TRUNCATED)
GCF_000013425.1
1
93,061
Staphylococcus aureus subsp. aureus
S. aureus
NC_007795.1
2,821,361
Staphylococcus aureus subsp. aureus NCTC 8325 chromosome, complete genome
forward
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGGTCCGAAGCATGAGTGTTTACAATGTTCGAACACCTTA(...TRUNCATED)
GCF_000240185.1
6
1,125,630
Klebsiella pneumoniae subsp. pneumoniae
K. pneumoniae
NC_016838.1
122,799
Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS1, complete sequence
forward
"GTTCTCGTTTTAGTGATTGTTGACCGGAACCACGATAGCTTACTAGGCACACCTGTAATCGCAAATGCCTGTTTTACTTATCCACTTATCCACTGGTTA(...TRUNCATED)
GCF_000240185.1
8
1,125,630
Klebsiella pneumoniae subsp. pneumoniae
K. pneumoniae
NC_016839.1
105,974
Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS3, complete sequence
forward
"TATGTGGGAACGCTGCACGAAAGCTCTGTTTTGTAAGGATTTTGTGGAAAAAAGAGGGGTTCCGTGTGGATAACAGTGGATAAGATCCAAGGGTATGTG(...TRUNCATED)
GCF_000240185.1
9
1,125,630
Klebsiella pneumoniae subsp. pneumoniae
K. pneumoniae
NC_016840.1
3,751
Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS4, complete sequence
forward
"TTTTTGAGCAGCGGGCTTTCCGGCGGTTTTCTCCTCTCAGCCCAGCAATGGTGCGGCCTACCGCATGATTGAGGTGGTCGTGCTCGCCGCAGTCTCATG(...TRUNCATED)
GCF_000240185.1
11
1,125,630
Klebsiella pneumoniae subsp. pneumoniae
K. pneumoniae
NC_016841.1
1,308
Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS6, complete sequence
forward
"CGGAACCCCTGAAGGGGCCCCCACGATTTTTCGGTTGCCAATGGTTAAATTTTCACCGTTTTTTGCCCGACTGAAAGGAGGGTGCTACCTGGAGATCTC(...TRUNCATED)
GCF_000240185.1
5
1,125,630
Klebsiella pneumoniae subsp. pneumoniae
K. pneumoniae
NC_016845.1
5,333,942
Klebsiella pneumoniae subsp. pneumoniae HS11286 chromosome, complete genome
forward
"GGTGGTCTGCCTCGCATAAAGCGGTATGAAAATGGATTGAAGCCCGGGCCGTGGATTCTACTCAACTTTCGTCTTTCGAGAAAGACTCCGGGATCCTGA(...TRUNCATED)
GCF_000240185.1
7
1,125,630
Klebsiella pneumoniae subsp. pneumoniae
K. pneumoniae
NC_016846.1
111,195
Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS2, complete sequence
forward
"TTCAATGCCTATGGGTAAATTTTTACCCACCCATAATGACAGTGAAAACAGAAATTGCAAGCTATCGCGATACTTATCCACCGGAAAAATCTGCACTTT(...TRUNCATED)
GCF_000240185.1
10
1,125,630
Klebsiella pneumoniae subsp. pneumoniae
K. pneumoniae
NC_016847.1
3,353
Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS5, complete sequence
forward
"CCATTGTTGTAAATAAGGAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGGTATTTTTAGTGGTGAGGAGCGTTCAGAGATCTGGCGATTTTTGGGA(...TRUNCATED)
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pretty_name: ESKAPE contigs (ProkBERT-ready) tags: - genomics - dna - bacteria - eskape - transformers - prokbert - contrastive-learning task_categories: - feature-extraction - text-classification license: other language: - en

ESKAPE contigs (ProkBERT-ready)

Dataset summary

This dataset contains nucleotide contigs/genomes for ESKAPE pathogens, packaged for transformer-based modeling (e.g., ProkBERT). It includes NCBI taxonomy identifiers and compact scientific labels that are convenient for visualization.

Data structure

Rows

Each row corresponds to one contig (chromosome or plasmid) from an assembly.

Columns

  • assembly (str): Assembly accession (e.g., GCF_...).
  • taxon (int): NCBI Taxonomy ID.
  • taxon_name (str): Parsed scientific name (Genus species [+ subsp.]).
  • taxon_short (str): Short visualization label (e.g., E. coli MG1655).
  • contig (str): Contig accession/identifier.
  • description (str): NCBI contig description.
  • seq (str): Nucleotide sequence (uppercase).
  • seq_len (int): Sequence length.

Intended use

  • Pretraining / representation learning on bacterial genomes/contigs.
  • Supervised or weakly-supervised tasks with taxon-level labels.
  • Benchmarking sequence encoders and contrastive objectives.

Notes / caveats

  • taxon_name and taxon_short are derived heuristically from the contig description to standardize labels for plots. If you need strict taxonomy-name mapping, resolve taxon via an authoritative taxonomy dump/API.
  • Verify licensing/redistribution constraints for your specific upstream sources before downstream redistribution.

Usage 

from datasets import load_dataset

ds = load_dataset("neuralbioinfo/eskapee")
ds["train"][0]

Contact Information

For any questions, feedback, or contributions regarding the datasets or ProkBERT, please feel free to reach out:

We welcome your input and collaboration to improve our resources and research.

Citation 

@Article{ProkBERT2024,
  author  = {Ligeti, Balázs et al.},
  journal = {Frontiers in Microbiology},
  title   = {{ProkBERT} family: genomic language models},
  year    = {2024},
  volume  = {14},
  URL     = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1331233},
  DOI     = {10.3389/fmicb.2023.1331233}
}
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