metadata

dataset_info:
  features:
    - name: sequence_id
      dtype: int64
    - name: dataset
      dtype: string
    - name: description
      dtype: string
    - name: label
      dtype: string
    - name: 'y'
      dtype: int64
    - name: sequence
      dtype: string
    - name: __index_level_0__
      dtype: int64
  splits:
    - name: ESCHERICHIA_SEQDB
      num_bytes: 22428612
      num_examples: 394
    - name: EXTREMOPHILE_SEQDB
      num_bytes: 739732
      num_examples: 16
    - name: BACPHLIP_TRAINING_SEQDB
      num_bytes: 121740866
      num_examples: 1868
    - name: BACPHLIP_VALIDATION_SEQDB
      num_bytes: 19956326
      num_examples: 246
  download_size: 76237700
  dataset_size: 164865536
configs:
  - config_name: default
    data_files:
      - split: ESCHERICHIA_SEQDB
        path: data/ESCHERICHIA_SEQDB-*
      - split: EXTREMOPHILE_SEQDB
        path: data/EXTREMOPHILE_SEQDB-*
      - split: BACPHLIP_TRAINING_SEQDB
        path: data/BACPHLIP_TRAINING_SEQDB-*
      - split: BACPHLIP_VALIDATION_SEQDB
        path: data/BACPHLIP_VALIDATION_SEQDB-*

Dataset Card for `neuralbioinfo/PhaStyle-SequenceDB`

Dataset Summary

The PhaStyle-SequenceDB dataset consists of phage sequences labeled with their corresponding lifestyles (virulent or temperate). The dataset is split into four key subsets:

BACPHLIP training set: 1868 sequences for model training
BACPHLIP validation set: 394 Escherichia coli sequences for validation
EXTREMOPHILE set: 16 sequences from extreme environments
ESCHERICHIA set: Guelin collection + 100 randomly selected high-quality temperate phages

This dataset is specifically designed to aid in training and evaluating genomic models, such as ProkBERT, for phage lifestyle prediction.

Dataset Structure

The structure of the dataset is explained visually in the following figure:

Figure 1: The dataset used in the ProkBERT PhaStyle study. Phage sequences from multiple independent data sources were segmented into 512bp and 1022bp fragments for training and testing models on phage lifestyle prediction. The dataset consists of the BACPHLIP training and validation sets, Escherichia phages (from the Guelin collection), and phages from extreme environments.

ESCHERICHIA_SEQDB: Contains 394 E. coli sequences from the Guelin collection and 100 additional temperate phages. Each sequence is labeled as either virulent or temperate.
EXTREMOPHILE_SEQDB: Contains 16 phages from extreme environments (e.g., deep-sea, acidic environments). These sequences are split into segments of 512bp and 1022bp for analysis.
BACPHLIP_TRAINING_SEQDB: The training set for BACPHLIP, consisting of 1868 sequences labeled for phage lifestyle classification.
BACPHLIP_VALIDATION_SEQDB: The validation set for BACPHLIP, containing 394 sequences used to validate the performance of the models.

Data Fields

sequence_id: Unique identifier for each sequence.
dataset: The specific dataset the sequence belongs to (e.g., ESCHERICHIA, EXTREMOPHILE, BACPHLIP_TRAINING).
description: Additional details about the sequence, such as its classification or length.
label: Indicates the lifestyle of the phage (virulent or temperate).
y: Numerical encoding of the lifestyle (1 for virulent, 0 for temperate).
sequence: The nucleotide sequence of the phage.

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:

@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}
}

Dataset Card for neuralbioinfo/PhaStyle-SequenceDB