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}
}