macwiatrak/bacbench-essential-genes-protein-sequences

Dataset for essential genes prediction in bacterial genomes (Protein sequences)

A dataset of 169,408 genes with gene essentiality labels (binary) from 51 bacterial genomes across 37 species.

The gene essentiality labels have been extracted from the Database of Essential Genes and the protein sequences have been extracted from GenBank. Each row contains protein sequences present in the genome with an associated essentiality label. We excluded duplicates and genomes with incomplete genomes.

Labels

The labels for each gene are provided in the dataset in the essential column.

Usage

We recommend loading the dataset in a streaming mode to prevent memory errors.

from datasets import load_dataset


ds = load_dataset("macwiatrak/bacbench-essential-genes-protein-sequences", split="validation")

# fetch an example
item = ds[0]
# get gene sequences
gene_prot_seqs = item["sequence"]
# get labels
labels = item["essential"]

Split

We provide 60 / 20 /20 (%) train, validation and test splits respectively as part of the dataset. The split has been performed by randomly.

See github repository for details on how to embed the dataset with DNA and protein language models as well as code to predict gene essentiality. For DNA sequence representation of the genome see the macwiatrak/bacbench-essential-genes-dna dataset.

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dataset_info: features: - name: genome_name dtype: string - name: protein_id sequence: string - name: product sequence: string - name: sequence sequence: string - name: start sequence: float64 - name: end sequence: float64 - name: essential sequence: string - name: index_level_0 dtype: int64 splits: - name: train num_bytes: 40286383 num_examples: 30 - name: validation num_bytes: 15351889 num_examples: 11 - name: test num_bytes: 12146314 num_examples: 10 download_size: 59215919 dataset_size: 67784586 configs: - config_name: default data_files: - split: train path: data/train-* - split: validation path: data/validation-* - split: test path: data/test-*