---
dataset_info:
  features:
  - name: segment_id
    dtype: int64
  - name: sequence_id
    dtype: int64
  - name: class_label
    dtype: string
  - name: y
    dtype: int64
  - name: orientation
    dtype: string
  - name: Ls
    dtype: int64
  - name: segment_start
    dtype: int64
  - name: segment_end
    dtype: int64
  - name: test_fastaid
    dtype: string
  - name: segment
    dtype: string
  splits:
  - name: segmentdb_512
    num_bytes: 26884526
    num_examples: 43754
  - name: segmentdb_1022
    num_bytes: 24610284
    num_examples: 21922
  download_size: 20738792
  dataset_size: 51494810
configs:
- config_name: default
  data_files:
  - split: segmentdb_512
    path: data/segmentdb_512-*
  - split: segmentdb_1022
    path: data/segmentdb_1022-*
---

---
dataset_name: neuralbioinfo/PhaStyle-ESCHERICHIA
task: Phage Lifestyle Prediction
size: 65,676 rows
modality: Tabular
languages: Nucleotide Sequences
---

## Dataset Card for neuralbioinfo/PhaStyle-ESCHERICHIA

### Dataset Summary

The **neuralbioinfo/PhaStyle-ESCHERICHIA** dataset consists of phage sequences from the *Escherichia* genus, processed into 512bp and 1022bp segments. The dataset was used for evaluating the generalization performance of the ProkBERT PhaStyle model, specifically for predicting phage lifestyle (virulent or temperate) based on nucleotide sequences.

The dataset is divided into two splits:
- **segmentdb_512**: 43,800 rows (512bp segments)
- **segmentdb_1022**: 21,900 rows (1022bp segments)

### Dataset Structure

Each entry in the dataset contains the following fields:
- **segment_id**: Unique identifier for each segment
- **sequence_id**: Identifier for the original sequence
- **label**: Phage lifestyle label, either 'virulent' or 'temperate'
- **y**: Numeric representation of the label (1 for virulent, 0 for temperate)
- **orientation**: Whether the sequence is in forward or reverse-complement orientation
- **Ls**: Length of the segment (512 or 1022bp)
- **segment_start**: Start position of the segment within the original sequence

### Dataset Usage

The dataset is suitable for training and evaluating models on phage lifestyle prediction tasks. Each segment is labeled as either **virulent** or **temperate**.

### Dataset Splits

| Split Name        | Number of Rows |
|-------------------|----------------|
| segmentdb_512     | 43,800         |
| segmentdb_1022    | 21,900         |

### Data Fields

- **segment_id**: A unique identifier for each segmented entry.
- **sequence_id**: The ID of the original sequence from which the segment is derived.
- **label**: The lifestyle prediction for the phage (either virulent or temperate).
- **y**: Numeric encoding of the lifestyle label (1 for virulent, 0 for temperate).
- **orientation**: Indicates the orientation (forward or reverse-complement) of the sequence.
- **Ls**: The length of the segment in base pairs (512 or 1022).
- **segment_start**: The start position of the segment within the original sequence.

### Licensing

This dataset is provided under the same license as the ProkBERT PhaStyle repository. Please refer to the [license](https://github.com/nbrg-ppcu/PhaStyle) for more details.


### Citation

@article{ProkBERT2024,
  author = {Ligeti, Balázs and Szepesi-Nagy, István and Bodnár, Babett and Ligeti-Nagy, Noémi and Juhász, János},
  journal = {Frontiers in Microbiology},
  title = {ProkBERT family: Genomic language models for microbiome applications},
  year = {2024},
  volume = {14},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1331233},
  doi = {10.3389/fmicb.2023.1331233},
  issn = {1664-302X}
}