neuralbioinfo/PhaStyle-ESCHERICHIA

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dataset_name: neuralbioinfo/PhaStyle-ESCHERICHIA task: Phage Lifestyle Prediction size: 65,676 rows modality: Tabular languages: Nucleotide Sequences

Dataset Card for neuralbioinfo/PhaStyle-ESCHERICHIA

Dataset Summary

The neuralbioinfo/PhaStyle-ESCHERICHIA dataset consists of phage sequences from the Escherichia genus, processed into 512bp and 1022bp segments. The dataset was used for evaluating the generalization performance of the ProkBERT PhaStyle model, specifically for predicting phage lifestyle (virulent or temperate) based on nucleotide sequences.

The dataset is divided into two splits:

• segmentdb_512: 43,800 rows (512bp segments)
• segmentdb_1022: 21,900 rows (1022bp segments)

Dataset Structure

Each entry in the dataset contains the following fields:

• segment_id: Unique identifier for each segment
• sequence_id: Identifier for the original sequence
• label: Phage lifestyle label, either 'virulent' or 'temperate'
• y: Numeric representation of the label (1 for virulent, 0 for temperate)
• orientation: Whether the sequence is in forward or reverse-complement orientation
• Ls: Length of the segment (512 or 1022bp)
• segment_start: Start position of the segment within the original sequence

Dataset Usage

The dataset is suitable for training and evaluating models on phage lifestyle prediction tasks. Each segment is labeled as either virulent or temperate.

Dataset Splits

Split Name	Number of Rows
segmentdb_512	43,800
segmentdb_1022	21,900

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.
• label: The lifestyle prediction for the phage (either virulent or temperate).
• y: Numeric encoding of the lifestyle label (1 for virulent, 0 for temperate).
• orientation: Indicates the orientation (forward or reverse-complement) of the sequence.
• Ls: The length of the segment in base pairs (512 or 1022).
• segment_start: The start position of the segment within the original sequence.

Licensing

This dataset is provided under the same license as the ProkBERT PhaStyle repository. Please refer to the license 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} }