Datasets:
license: cc-by-nc-4.0
tags:
- genomics
- ESKAPE pathogens
- bioinformatics
- ProkBERT
dataset_info:
features:
- name: contig_id
dtype: string
- name: segment_id
dtype: string
- name: strand
dtype: string
- name: seq_start
dtype: int64
- name: seq_end
dtype: int64
- name: segment_start
dtype: int64
- name: segment_end
dtype: int64
- name: label
dtype: string
- name: segment_length
dtype: int64
- name: Nsegment
dtype: int64
- name: segment
dtype: string
splits:
- name: ESKAPE
num_bytes: 19414538
num_examples: 55653
download_size: 7614923
dataset_size: 19414538
configs:
- config_name: default
data_files:
- split: ESKAPE
path: data/ESKAPE-*
Dataset Card for ESKAPE Genomic Features Dataset
Dataset Description
This dataset includes genomic segments from ESKAPE pathogens, characterized by various genomic features such as coding sequences (CDS), intergenic regions, ncRNA, and pseudogenes. It was analyzed to understand the representations captured by models like ProkBERT-mini, ProkBERT-mini-c, and ProkBERT-mini-long.
Data Fields
contig_id: Identifier of the contig.segment_id: Unique identifier for each genomic segment.strand: DNA strand of the segment (+or-).seq_start: Starting position of the segment in the contig.seq_end: Ending position of the segment in the contig.segment_start: Starting position of the segment in the sequence.segment_end: Ending position of the segment in the sequence.label: Genomic feature category (e.g., CDS, intergenic).segment_length: Length of the genomic segment.Nsegment: [Additional description needed].segment: Genomic sequence of the segment.
UMAP Embeddings and Silhouette Scores
The dataset was used to assess the zero-shot capabilities of the ProkBERT models in predicting genomic features. UMAP technique was employed to reduce dimensionality and derive embeddings, which were then evaluated using silhouette scores. The embeddings and scores reveal the models' proficiency in differentiating between genomic features and capturing the genomic structure of ESKAPE pathogens.
Dataset Creation
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. The segment length is 256, shorter fragments were discarded.
Overview of ESKAPE Pathogens
ESKAPE pathogens are a group of bacteria that pose a significant threat to public health due to their high levels of antibiotic resistance. The acronym ESKAPE represents six genera of bacteria:
- Enterococcus faecium
- Staphylococcus aureus
- Klebsiella pneumoniae
- Acinetobacter baumannii
- Pseudomonas aeruginosa
- Enterobacter species
These pathogens are known for "escaping" the effects of antibiotics and are responsible for a large proportion of nosocomial infections (hospital-acquired infections). They are particularly concerning in healthcare settings because they can lead to severe infections that are increasingly difficult to treat due to their resistance to multiple antibiotics.
Public Health Implications
- Resistance to Treatment: ESKAPE pathogens often exhibit resistance to multiple classes of antibiotics, making infections difficult to treat and leading to higher morbidity and mortality rates.
- Hospital-Acquired Infections: These pathogens are commonly associated with infections acquired in healthcare settings, including pneumonia, bloodstream infections, urinary tract infections, and surgical site infections.
- Evolving Threat: The ability of these bacteria to rapidly evolve and acquire new resistance mechanisms poses a significant challenge for the development of effective treatments.
Considerations for Using the Data
This dataset is relevant for genomic research and bioinformatics, particularly for understanding the genomic structure of ESKAPE pathogens and their representation in embedding spaces.
Additional Information
Dataset Curators
Curated by [Your Team/Institution Name].
Licensing Information
Creative Commons Attribution Non-Commercial 4.0 International.