---
dataset_info:
  features:
  - name: genome_name
    dtype: string
  - name: contig_name
    sequence: string
  - name: protein_id
    sequence:
      sequence: string
  - name: protein_sequence
    sequence:
      sequence: string
  - name: taxid
    dtype: string
  - name: locus_tag
    sequence:
      sequence: string
  - name: start
    sequence:
      sequence: int64
  - name: end
    sequence:
      sequence: int64
  - name: product
    sequence:
      sequence: string
  - name: label
    dtype: float64
  splits:
  - name: train
    num_bytes: 778412387
    num_examples: 618
  - name: validation
    num_bytes: 261143933
    num_examples: 206
  - name: test
    num_bytes: 242498068
    num_examples: 206
  download_size: 1090641715
  dataset_size: 1282054388
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*
  - split: validation
    path: data/validation-*
  - split: test
    path: data/test-*
license: apache-2.0
pretty_name: >-
  Dataset for predicting Catalase phenotype from whole bacterial genomes
  (protein sequences)
tags:
- biology
- bacteria
- bacformer
- prokaryotes
- genomic
- genome
- protein
size_categories:
- 1K<n<10K
---

# Dataset for predicting Catalase phenotype from whole bacterial genomes (protein sequences)

A dataset of over 1k bacterial genomes across species with the Catalase as label. Catalase 
denotes whether a bacterium produces the catalase enzyme that breaks down hydrogen peroxide (H₂O₂) into water and oxygen, thereby protecting the cell from oxidative stress.
Here, we provide binary Catalase labels, therefore the problem is a binary classification problem.

The genome protein sequences have been extracted from GenBank. Each row contains a list of protein sequences present in the bacterial genome, ordered by their location on the chromosome and plasmids.

The phenotypic traits have been extracted from [1].

## Usage

Please see the [Finetuning Bacformer for phenotypic traits prediction tutorial](https://github.com/macwiatrak/Bacformer/blob/main/tutorials/finetune_phenotypic_traits_prediction_tutorial.ipynb) 
for an example on how to use the dataset.

## References

[1] Weimann, Aaron, et al. "From genomes to phenotypes: Traitar, the microbial trait analyzer." MSystems 1.6 (2016): 10-1128.