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--- |
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license: cc-by-nc-4.0 |
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language: |
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- en |
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tags: |
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- genomics |
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- phage-prediction |
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- bioinformatics |
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dataset_info: |
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features: |
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- name: segment_id |
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dtype: int64 |
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- name: contig_id |
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dtype: string |
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- name: segment_start |
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dtype: int64 |
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- name: segment_end |
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dtype: int64 |
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- name: L |
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dtype: int64 |
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- name: segment |
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dtype: string |
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- name: class_label |
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dtype: string |
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- name: y |
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dtype: int64 |
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splits: |
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- name: sample_test_L512 |
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num_bytes: 5940699 |
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num_examples: 10000 |
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- name: sample_test_L1024 |
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num_bytes: 11060262 |
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num_examples: 10000 |
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- name: sample_test_L2048 |
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num_bytes: 21299753 |
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num_examples: 10000 |
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download_size: 18115489 |
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dataset_size: 38300714 |
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configs: |
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- config_name: default |
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data_files: |
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- split: sample_test_L512 |
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path: data/sample_test_L512-* |
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- split: sample_test_L1024 |
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path: data/sample_test_L1024-* |
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- split: sample_test_L2048 |
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path: data/sample_test_L2048-* |
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--- |
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# Dataset Card for Phage Prediction Dataset |
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## Dataset Description |
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To train and assess our prediction models, we assembled a comprehensive phage sequence database from diverse sources. |
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As of July 9, 2023, we procured viral sequences and annotations from the RefSeq database. By isolating entries labeled 'phage', we obtained 6,075 contigs. |
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Our database was further enriched with the inclusion of the TemPhD database, adding another 192,326 phage contigs extracted from 148,229 assemblies. |
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To address sequence redundancy present in both the RefSeq and TemPhD databases, we applied the CD-HIT algorithm (using CD-HIT-EST with a default word size of 5). |
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While several clustering thresholds (0.99, 0.95, 0.90) were experimented with and found to produce similar outcomes, we settled on a threshold of 0.99. |
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This process resulted in a refined set of 40,512 distinct phage sequences, with an average length of approximately 43,356 base pairs, culminating in a total of 3.5 billion base pairs. |
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Notably, these sequences target a wide spectrum of 660 bacterial genera. Subsequent to sequence curation, phage sequences were mapped to their respective bacterial hosts. |
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It is a sample dataset consisting of 10,000 segments, representing random samples and segments of phage genomes. |
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The full dataset is available on [Zenodo](https://zenodo.org/records/10057832). |
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## Features |
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- **Phage-Host Associations**: Our dataset represents bacteriophages and their bacterial hosts. |
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- **Balanced Representation**: The dataset is structured to mitigate bias by evenly representing phages and their hosts across various genera, incorporating reverse-complement sequences for completeness. |
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- **Dataset Composition**: The final collection includes sequences of varying lengths to accommodate different research needs, with a balanced distribution across training, validation, and testing sets. |
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- **Sampling Strategy**: To ensure a comprehensive yet manageable dataset, we performed undersampling and upsampling techniques, creating a diverse array of sequence lengths and ensuring no overlap between training and testing sets at the species level. |
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### Dataset Structure |
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The dataset is divided into three subsets based on segment lengths: 512, 1024, and 2048 base pairs. These subsets are named `sample_test_L512`, `sample_test_L1024`, and `sample_test_L2048`, respectively. |
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#### Data Fields |
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- `segment_id`: Unique identifier for each genomic segment. |
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- `contig_id`: Identifier for the contig from which the segment is derived. |
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- `segment_start`: Start position of the segment in the contig. |
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- `segment_end`: End position of the segment in the contig. |
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- `L`: Length of the genomic segment (512, 1024, or 2048). |
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- `segment`: The genomic sequence of the segment. |
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- `label`: Classification label (e.g., 'phage'). |
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- `y`: Binary label (1 for phage, 0 for non-phage). |
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### Data Splits |
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The dataset is structured as follows: |
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- `sample_test_L512`: Test set with segment length of 512. |
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- `sample_test_L1024`: Test set with segment length of 1024. |
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- `sample_test_L2048`: Test set with segment length of 2048. |
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## Dataset Creation |
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### Source Data |
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The dataset is compiled from diverse genomic sources, with a focus on phage sequences and annotations from the RefSeq database and a dataset validated through the TemPhD method. Redundancy in sequences is addressed using the CD-HIT algorithm. |
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## Contact Information |
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For any questions, feedback, or contributions regarding the datasets or ProkBERT, please feel free to reach out: |
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- **Name**: Balázs Ligeti |
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- **Email**: obalasz@gmail.com |
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We welcome your input and collaboration to improve our resources and research. |
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## Citation |
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```bibtex |
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@Article{ProkBERT2024, |
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author = {Ligeti, Balázs et al.}, |
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journal = {Frontiers in Microbiology}, |
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title = {{ProkBERT} family: genomic language models}, |
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year = {2024}, |
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volume = {14}, |
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URL = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1331233}, |
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DOI = {10.3389/fmicb.2023.1331233} |
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} |
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