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---
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}
}
```
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