---
license: apache-2.0
tags:
- bacteria
- gene_essentiality
- genes
- genomics
- genomes
- prokaryotes
- biology
pretty_name: >-
  Dataset for predicting essential genes in bacterial genomes (protein
  sequences)
size_categories:
- n<1K
---
# 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](http://origin.tubic.org/deg/public/index.php/browse/bacteria) and the protein sequences have been extracted from [GenBank](https://www.ncbi.nlm.nih.gov/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.
```python
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](https://github.com/macwiatrak/Bacbench) 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](https://huggingface.co/datasets/macwiatrak/bacbench-essential-genes-dna)
dataset.

---
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-*
---