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--- |
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language: |
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- en |
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license: mit |
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task_categories: |
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- text-generation |
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size_categories: |
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- 100K<n<1M |
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configs: |
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- config_name: default |
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data_files: "*.parquet" |
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default: true |
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--- |
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# LOL-EVE Ultra Rare Variants Dataset |
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## Dataset Description |
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This dataset contains ultra rare variants from gnomAD for evaluating variant effect prediction models. The dataset includes variants with minor allele frequency (MAF) < 0.001 in promoter regions across diverse genes. |
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## Dataset Structure |
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- **Total Variants**: ~549,000 |
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- **Species**: Primates (Homo sapiens) |
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- **Variant Types**: Insertions, deletions, and substitutions in promoter regions |
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- **Sequence Length**: Up to 1,000bp promoter regions |
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- **MAF Range**: < 0.001 (ultra rare) |
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## Features |
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### Basic Variant Information |
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- `gene`: Gene symbol |
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- `species`: Species name |
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- `clade`: Evolutionary clade |
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- `chromosome`: Chromosome |
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- `position`: Genomic position |
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- `ref`: Reference allele |
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- `alt`: Alternative allele |
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- `variant_type`: Type of variant (insertion/deletion/substitution) |
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### Sequences |
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- `wt_sequence`: Wild-type sequence |
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- `var_sequence`: Variant sequence |
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- `sequence_length`: Length of sequence |
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- `wt_sequence_start`: Start position of sequence |
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### Variant Annotations |
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- `filter`: Variant filtering status |
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- `maf`: Minor allele frequency |
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## Usage |
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```python |
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from datasets import load_dataset |
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# Load the dataset |
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dataset = load_dataset("cshearer/LOL-EVE-UltraRare") |
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# Access the data |
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print(f"Dataset size: {len(dataset['train'])}") |
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print(f"Features: {dataset['train'].features}") |
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# Example: Get variants by MAF threshold |
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rare_variants = dataset['train'].filter(lambda x: x['maf'] < 0.0001) |
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print(f"Ultra rare variants (MAF < 0.0001): {len(rare_variants)}") |
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# Example: Get variants by type |
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insertions = dataset['train'].filter(lambda x: x['variant_type'] == 'insertion') |
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deletions = dataset['train'].filter(lambda x: x['variant_type'] == 'deletion') |
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substitutions = dataset['train'].filter(lambda x: x['variant_type'] == 'substitution') |
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``` |
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## Citation |
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If you use this dataset in your research, please cite: |
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```bibtex |
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@article{loleve2024, |
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title={LOL-EVE: Language of Life - Evolutionary Variant Effects}, |
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author={Your Name and Collaborators}, |
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journal={Nature}, |
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year={2024} |
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} |
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``` |
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## License |
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This dataset is released under the MIT License. |
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