README.md

---
dataset_info:
  features:
  - name: sequence_id
    dtype: int64
  - name: dataset
    dtype: string
  - name: class_label
    dtype: string
  - name: y
    dtype: int64
  - name: source_fasta_id
    dtype: string
  - name: orientation
    dtype: string
  - name: test_fastaid
    dtype: string
  - name: L_seq
    dtype: int64
  - name: source_description
    dtype: string
  - name: Genome type
    dtype: string
  - name: Family
    dtype: string
  - name: subds_seqid
    dtype: int64
  - name: sequence
    dtype: string
  - name: __index_level_0__
    dtype: int64
  splits:
  - name: BACPHLIP_TRAINING
    num_bytes: 116974286
    num_examples: 1798
  - name: BACPHLIP_VALIDATION
    num_bytes: 24907540
    num_examples: 316
  - name: ESCHERICHIA
    num_bytes: 22460394
    num_examples: 394
  - name: EXTREMOPHILE
    num_bytes: 740980
    num_examples: 16
  - name: BACPHLIP_ALL
    num_bytes: 141860532
    num_examples: 2114
  - name: BASEL
    num_bytes: 26560728
    num_examples: 412
  download_size: 154452219
  dataset_size: 333504460
configs:
- config_name: default
  data_files:
  - split: BACPHLIP_TRAINING
    path: data/BACPHLIP_TRAINING-*
  - split: BACPHLIP_VALIDATION
    path: data/BACPHLIP_VALIDATION-*
  - split: ESCHERICHIA
    path: data/ESCHERICHIA-*
  - split: EXTREMOPHILE
    path: data/EXTREMOPHILE-*
  - split: BACPHLIP_ALL
    path: data/BACPHLIP_ALL-*
  - split: BASEL
    path: data/BASEL-*
---
# Dataset Card for `neuralbioinfo/PhaStyle-SequenceDB`

# phastyle Sequence Database

A collection of bacteriophage nucleotide sequences and metadata for training and evaluating phage lifestyle prediction models. Available splits support both **strict-holdout** and **standard-holdout** experiments.

## Dataset Features

| Name                | Type    | Description                                                      |
|---------------------|---------|------------------------------------------------------------------|
| `sequence_id`       | `int64` | Unique integer identifier for each sequence                      |
| `dataset`           | `string`| Source collection name (see “Splits” below)                      |
| `class_label`       | `string`| Lifestyle label: `"temperate"` or `"virulent"`                   |
| `y`                 | `int64` | Binary label: `0` = temperate, `1` = virulent                    |
| `source_fasta_id`   | `string`| Original FASTA record ID                                         |
| `orientation`       | `string`| Strand orientation: `"forward"` or `"reverse_complement"`        |
| `test_fastaid`      | `string`| FASTA ID used in the test split (if applicable)                 |
| `L_seq`             | `int64` | Sequence length in base pairs                                    |
| `source_description`| `string`| Free‐text description of isolate or environment                  |
| `Genome type`       | `string`| “dsDNA”, “ssDNA”, etc.                                           |
| `Family`            | `string`| Taxonomic family                                                 |
| `subds_seqid`       | `int64` | Sub‐dataset sequence index (internal use)                        |
| `sequence`          | `string`| Nucleotide sequence                                              |

## Splits

- **BACPHLIP_TRAINING** (1,798 examples, 116 MB)  
  - Used for **strict-holdout** training (excludes any *Escherichia*-infecting phages or ≥ 80 % ANI to test set).  
- **BACPHLIP_VALIDATION** (316 examples, 25 MB)  
  - *Escherichia* phages held out for validation in the strict-holdout setting.  
- **BACPHLIP_ALL** (2,114 examples, 142 MB)  
  - Used for **standard-holdout** training (no ANI or host exclusions).  
- **ESCHERICHIA** (394 examples, 22 MB)  
  - Guelin collection: experimentally validated *Escherichia* phages.  
- **BASEL** (412 examples, 27 MB)  
  - BASEL collection: environmental *E. coli* isolates.  
- **EXTREMOPHILE** (16 examples, 0.8 MB)  
  - Phages from deep‐sea, acidic, and arsenic‐rich environments.

## Dataset Creation

The sequences in this dataset were gathered from various sources, including the BACPHLIP database and curated collections of phages from extreme environments. Each sequence was carefully segmented into smaller fragments (512bp or 1022bp) to simulate real-world scenarios where phage sequences are often fragmented. The training data excludes Escherichia sequences, which are used in the test set to evaluate model generalization capabilities.

## Intended Uses

This dataset is intended for use in phage lifestyle prediction tasks using genomic language models such as ProkBERT. The segmented sequences allow models to generalize well even with fragmented or out-of-sample data. It is particularly useful for applications in ecological and clinical settings where understanding phage behavior is critical.

# Citing this work

If you use the data in this package, please cite:

```bibtex
@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}
}
```