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
@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}
}