Update README.md

README.md

@@ -42,3 +42,38 @@ configs:
   - 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
+
+- **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.