neuralbioinfo/ESKAPE-masking

Dataset Description

This dataset was used to evaluate different models on the masking exercise, measuring how well the different models can 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 contiguous segmentation. This dataset contains various segments with lengths: [128, 256, 512, 1024]. The segments were randomly selected, and one of the characters was replaced by '*' (masked_segment column) to create a masking task. The reference_segment contains the original, non-replaced nucleotides. We performed 10,000 maskings per set, with a maximum of 2,000 genomic features. Only the genomic features: 'CDS', 'intergenic', 'pseudogene', and 'ncRNA' 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. (unique only with respect to length)
• contig_id: Identifier of the contig to which the segment belongs.
• segment_id: Unique identifier for each genomic segment (same as 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 use this dataset in the development and evaluation of bioinformatics models, especially those related to genomic studies.

Contact Information

For any questions, feedback, or contributions regarding the datasets or ProkBERT, please feel free to reach out:

• Name: Balázs Ligeti
• Email: obalasz@gmail.com

We welcome your input and collaboration to improve our resources and research.

Citation

@Article{ProkBERT2024,
  author  = {Ligeti, Balázs et al.},
  journal = {Frontiers in Microbiology},
  title   = {{ProkBERT} family: genomic language models},
  year    = {2024},
  volume  = {14},
  URL     = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1331233},
  DOI     = {10.3389/fmicb.2023.1331233}
}