---
license: cc-by-4.0
dataset_info:
  features:
  - name: segment_id
    dtype: int64
  - name: sequence_id
    dtype: int64
  - name: ncbi_acc
    dtype: string
  - name: class_label
    dtype: string
  - name: y
    dtype: int64
  - name: description
    dtype: string
  - 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: 988584
    num_examples: 1440
  - name: segmentdb_1022
    num_bytes: 863980
    num_examples: 724
  download_size: 746526
  dataset_size: 1852564
configs:
- config_name: default
  data_files:
  - split: segmentdb_512
    path: data/segmentdb_512-*
  - split: segmentdb_1022
    path: data/segmentdb_1022-*
---

# PhaStyle-EXTREMOPHILE Dataset

## Description

The PhaStyle-EXTREMOPHILE dataset is a **test dataset** used for evaluating the ProkBERT PhaStyle model for phage lifestyle prediction. It contains phages isolated from extreme environments such as deep-sea, acidic, and arsenic-rich habitats. This dataset includes phage sequences that have been segmented into 512bp and 1022bp fragments to simulate fragmented metagenomic assemblies. These phages were not included in the training dataset, making this a crucial benchmark for testing the model's generalization ability to unseen data.

The dataset is primarily used to classify phages as either **virulent** or **temperate** and has been evaluated using genomic language modeling approaches such as ProkBERT PhaStyle.

## Dataset Splits

| Split Name          | Number of Rows | Segment Length |
| ------------------- | -------------- | -------------- |
| segmentdb_512       | 1,440          | 512 bp         |
| segmentdb_1022      | 724            | 1022 bp        |

## 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.
- **ncbi_acc**: The NCBI accession number of the phage sequence.
- **label**: The lifestyle prediction for the phage (either virulent or temperate).
- **y**: Numeric encoding of the lifestyle label (1 for virulent, 0 for temperate).
- **description**: Description of the environment from which the phage was isolated.
- **orientation**: Indicates the orientation (forward or reverse-complement) of the sequence.
- **Ls**: The length of the segment in base pairs (512 or 1022 max).
- **segment_start**: The start position of the segment within the original sequence.
- **segment_end**: The end position of the segment within the original sequence.
- **test_fastaid**: The FASTA identifier for the test set.
- **segment**: The nucleotide sequence of the segment.

## Phage Overview

The following table summarizes the phages in the EXTREMOPHILE dataset, their environments, and lifestyles:

| Viral Family          | Habitat                               | NCBI Acc.     | Lifestyle   |
| --------------------- | ------------------------------------- | ------------- | ----------- |
| Autographiviridae      | Arsenic-rich environments (Psychrotolerant) | OM913597.1    | Virulent    |
|                       |                                       | OM913598.1    | Virulent    |
|                       |                                       | OM913599.1    | Virulent    |
| Unk. Caudoviricetes    | Deep subseafloor sediments (381 m)    | JF974314.1    | Temperate   |
|                       |                                       | JF974315.1    | Temperate   |
|                       | Deep-sea (1000 m)                     | AB967974.1    | Temperate   |
| Suviridae              | Hadal, Mariana Trench (8,900 m)       | OQ832096.1    | Temperate   |
| Myoviridae             | Biomining biotopes, highly acidic environments | JX507079.1    | Temperate   |

*Figure 1: Overview of phages from extreme environments used in the PhaStyle-EXTREMOPHILE test dataset.* 


## Licensing

This dataset is licensed under **cc-by-4.0**. Please refer to the licensing terms for more details.



## Citation

```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}
}
```