Datasets:

neuralbioinfo
/

PhaStyle-SequenceDB

@@ -68,46 +68,42 @@ configs:
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 # 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
-<img src="https://github.com/nbrg-ppcu/PhaStyle/blob/main/assets/figure_01.jpg?raw=true" alt="Dataset Structure" width="600"/>
-*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.*
-The structure of the dataset is explained visually in the following figure:
-- **BACPHLIP Training Set**: This subset consists of **1,868 phage sequences** collected from non-Escherichia phages. The sequences are carefully labeled as virulent or temperate, and the dataset was constructed using the high-quality annotations from the **BACPHLIP** study. These sequences are used to train the ProkBERT model for lifestyle prediction.
-- **BACPHLIP Validation Set**: Comprising **246 Escherichia phage sequences**, this validation set is used to test the performance of the model after training. The sequences are also labeled based on their lifestyle and are critical for evaluating the generalization capability of the ProkBERT model on Escherichia species.
-- **ESCHERICHIA (Guelin collection + 100 high-quality phages)**: This dataset contains **394 Escherichia phages**, which includes the Guelin collection and an additional 100 randomly selected, high-quality temperate phages. The sequences are segmented into smaller chunks (512bp and 1022bp), representing real-world metagenome assemblies, often fragmented.
-- **EXTREMOPHILE Phage Set**: This test dataset consists of **16 bacteriophages** isolated from extreme environments like deep-sea, acidic environments, and arsenic-rich microbial mats. It represents underexplored environments, making it essential for testing how well the models generalize to novel phages outside the commonly studied species.
-## 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

 ---
 # Dataset Card for `neuralbioinfo/PhaStyle-SequenceDB`
+# phastyle Sequence Database
+A collection of bacteriophage nucleotide sequences and metadata for training and evaluating phage lifestyle prediction models. Available splits support both **strict-holdout** and **standard-holdout** experiments.
+## Dataset Features
+| Name                | Type    | Description                                                      |
+|---------------------|---------|------------------------------------------------------------------|
+| `sequence_id`       | `int64` | Unique integer identifier for each sequence                      |
+| `dataset`           | `string`| Source collection name (see “Splits” below)                      |
+| `class_label`       | `string`| Lifestyle label: `"temperate"` or `"virulent"`                   |
+| `y`                 | `int64` | Binary label: `0` = temperate, `1` = virulent                    |
+| `source_fasta_id`   | `string`| Original FASTA record ID                                         |
+| `orientation`       | `string`| Strand orientation: `"forward"` or `"reverse_complement"`        |
+| `test_fastaid`      | `string`| FASTA ID used in the test split (if applicable)                 |
+| `L_seq`             | `int64` | Sequence length in base pairs                                    |
+| `source_description`| `string`| Free‐text description of isolate or environment                  |
+| `Genome type`       | `string`| “dsDNA”, “ssDNA”, etc.                                           |
+| `Family`            | `string`| Taxonomic family                                                 |
+| `subds_seqid`       | `int64` | Sub‐dataset sequence index (internal use)                        |
+| `sequence`          | `string`| Nucleotide sequence                                              |
+## Splits
+- **BACPHLIP_TRAINING** (1,798 examples, 116 MB)
+  - Used for **strict-holdout** training (excludes any *Escherichia*-infecting phages or ≥ 80 % ANI to test set).
+- **BACPHLIP_VALIDATION** (316 examples, 25 MB)
+  - *Escherichia* phages held out for validation in the strict-holdout setting.
+- **BACPHLIP_ALL** (2,114 examples, 142 MB)
+  - Used for **standard-holdout** training (no ANI or host exclusions).
+- **ESCHERICHIA** (394 examples, 22 MB)
+  - Guelin collection: experimentally validated *Escherichia* phages.
+- **BASEL** (412 examples, 27 MB)
+  - BASEL collection: environmental *E. coli* isolates.
+- **EXTREMOPHILE** (16 examples, 0.8 MB)
+  - Phages from deep‐sea, acidic, and arsenic‐rich environments.
 ## Dataset Creation