dataset_info:
features:
- name: segment_id
dtype: int64
- name: sequence_id
dtype: int64
- name: label
dtype: string
- name: 'y'
dtype: int64
- 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: 26884526
num_examples: 43754
- name: segmentdb_1022
num_bytes: 24610284
num_examples: 21922
download_size: 20896660
dataset_size: 51494810
configs:
- config_name: default
data_files:
- split: segmentdb_512
path: data/segmentdb_512-*
- split: segmentdb_1022
path: data/segmentdb_1022-*
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} }