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--- |
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license: cc-by-nc-4.0 |
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tags: |
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- genomics |
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- ESKAPE pathogens |
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- bioinformatics |
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- ProkBERT |
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dataset_info: |
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features: |
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- name: contig_id |
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dtype: string |
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- name: segment_id |
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dtype: string |
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- name: strand |
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dtype: string |
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- name: seq_start |
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dtype: int64 |
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- name: seq_end |
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dtype: int64 |
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- name: segment_start |
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dtype: int64 |
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- name: segment_end |
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dtype: int64 |
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- name: label |
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dtype: string |
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- name: segment_length |
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dtype: int64 |
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- name: Nsegment |
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dtype: int64 |
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- name: segment |
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dtype: string |
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splits: |
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- name: ESKAPE |
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num_bytes: 19414538 |
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num_examples: 55653 |
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download_size: 7614923 |
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dataset_size: 19414538 |
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configs: |
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- config_name: default |
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data_files: |
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- split: ESKAPE |
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path: data/ESKAPE-* |
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--- |
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# Dataset Card for ESKAPE Genomic Features Dataset |
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## Dataset Description |
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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. |
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### Data Fields |
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- `contig_id`: Identifier of the contig. |
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- `segment_id`: Unique identifier for each genomic segment. |
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- `strand`: DNA strand of the segment (`+` or `-`). |
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- `seq_start`: Starting position of the segment in the contig. |
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- `seq_end`: Ending position of the segment in the contig. |
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- `segment_start`: Starting position of the segment in the sequence. |
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- `segment_end`: Ending position of the segment in the sequence. |
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- `label`: Genomic feature category (e.g., CDS, intergenic). |
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- `segment_length`: Length of the genomic segment. |
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- `Nsegment`: [Additional description needed]. |
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- `segment`: Genomic sequence of the segment. |
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### UMAP Embeddings and Silhouette Scores |
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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. |
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## Dataset Creation |
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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. |
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## Overview of ESKAPE Pathogens |
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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: |
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- **Enterococcus faecium** |
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- **Staphylococcus aureus** |
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- **Klebsiella pneumoniae** |
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- **Acinetobacter baumannii** |
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- **Pseudomonas aeruginosa** |
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- **Enterobacter species** |
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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. |
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### Public Health Implications |
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- **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. |
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- **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. |
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- **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. |
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## Considerations for Using the Data |
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This dataset is relevant for genomic research and bioinformatics, particularly for understanding the genomic structure of ESKAPE pathogens and their representation in embedding spaces. |
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## Additional Information |
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### Dataset Curators |
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Curated by [Your Team/Institution Name]. |
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### Licensing Information |
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Creative Commons Attribution Non-Commercial 4.0 International. |
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### Citation Information |
