Update README.md

README.md

@@ -42,3 +42,55 @@ configs:
   - split: train
     path: data/train-*
 ---
+
+# Dataset Description
+
+This dataset was used for evaluated the different models on the masking exercise, i.e. measuring how well the different models are able to recover the original character. 
+
+## Dataset Overview
+
+The dataset is compiled from the RefSeq database and other sources, focusing on ESKAPE pathogens. The genomic features were sampled randomly, followed by contigous segmentation. 
+This dataset contains various different segment with lengths: [128, 256, 512, 1024]. 
+The segments were randomly selected and one of the characters were replace by * (masked_segment column). The reference_segment contains the original, non-replaced nucleotides.
+We performed 10000 masking per set, maximum of 2000 genomic feeatures. Only the genomic features: 'CDS', 'intergenic', 'pseudogene', 'ncRNA' features were considered. 
+
+
+## Data Fields
+
+- `reference_segment_id`: A mapping of segment identifiers to their respective reference IDs in the database.
+- `masked_segment`: The DNA sequence of the segment with certain positions masked (marked with '*') for prediction or testing purposes.
+- `position_to_mask`: The specific position(s) in the sequence that have been masked, indicated by index numbers.
+- `masked_segment_id`: Unique identifiers assigned to the masked segments. (only unique with respect to length)
+- `contig_id`: Identifier of the contig to which the segment belongs.
+- `segment_id`: Unique identifier for each genomic segment. (reference segment id)
+- `strand`: The DNA strand of the segment, indicated as '+' (positive) or '-' (negative).
+- `seq_start`: Starting position of the segment within the contig.
+- `seq_end`: Ending position of the segment within the contig.
+- `segment_start`: Starting position of the genomic segment in the sequence.
+- `segment_end`: Ending position of the genomic segment in the sequence.
+- `label`: Category label for the genomic segment (e.g., 'CDS', 'intergenic').
+- `segment_length`: The length of the genomic segment.
+- `original_segment`: The original genomic sequence without any masking.
+
+
+## Usage
+
+This dataset is intended for academic and research purposes. Users are encouraged to apply this dataset in the development and evaluation of bioinformatics models, especially those related to genomic studies.
+
+## Citation
+
+
+If you use the code or data in this package, please cite:
+
+```bibtex
+@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}
+}
+```