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--- |
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license: mit |
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tags: |
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- biology |
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- genetics |
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- genomics |
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- variants |
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- annotation |
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- longevity |
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- pharmacogenomics |
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language: |
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- en |
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size_categories: |
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- 1K<n<10K |
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--- |
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# Genomic Variant Annotators |
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Curated genomic variant annotation modules from the [DNA-seq](https://github.com/dna-seq) project. |
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## Overview |
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This dataset contains pre-computed annotation data for genetic variants, organized by module: |
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| Module | Description | Files | |
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|--------|-------------|-------| |
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| longevitymap | Longevity-associated variants | annotations.parquet, studies.parquet, weights.parquet | |
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## Schema |
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### annotations.parquet |
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Variant-level facts linking rsIDs to genes and phenotypes. |
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- `rsid`: dbSNP reference ID |
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- `module`: Source module name |
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- `gene`: Associated gene symbol |
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- `phenotype`: Associated phenotype/trait |
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- `category`: Functional category |
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### studies.parquet |
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Per-study evidence from scientific publications. |
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- `rsid`: dbSNP reference ID |
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- `module`: Source module name |
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- `pmid`: PubMed ID |
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- `population`: Study population |
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- `p_value`: Statistical significance |
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- `conclusion`: Study conclusion |
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- `study_design`: Type of study |
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### weights.parquet |
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Curator-defined scoring for variant impact. |
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- `rsid`: dbSNP reference ID |
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- `genotype`: Genotype as list[str] (e.g., ["C", "T"]) |
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- `module`: Source module name |
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- `weight`: Numeric weight |
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- `state`: "protective", "risk", or "neutral" |
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- `priority`: Priority level |
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- `conclusion`: Curator conclusion |
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- `curator`: Curator name |
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- `method`: Curation method |
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## Usage |
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```python |
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import polars as pl |
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# Load from HuggingFace |
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weights = pl.read_parquet("hf://datasets/just-dna-seq/annotators/data/longevitymap/weights.parquet") |
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studies = pl.read_parquet("hf://datasets/just-dna-seq/annotators/data/longevitymap/studies.parquet") |
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annotations = pl.read_parquet("hf://datasets/just-dna-seq/annotators/data/longevitymap/annotations.parquet") |
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``` |
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## Statistics |
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- **Modules**: 1 (longevitymap) |
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- **Total files**: 3 |
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- **Total size**: 0.10 MB |
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## License |
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MIT License - See [LICENSE](LICENSE) for details. |
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## Citation |
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If you use this data, please cite the original sources: |
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- LongevityMap: [https://longevitymap.org/](https://longevitymap.org/) |
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