| --- |
| license: mit |
| tags: |
| - biology |
| - genetics |
| - genomics |
| - variants |
| - annotation |
| - longevity |
| - pharmacogenomics |
| language: |
| - en |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # Genomic Variant Annotators |
|
|
| Curated genomic variant annotation modules from the [DNA-seq](https://github.com/dna-seq) project. |
|
|
| ## Overview |
|
|
| This dataset contains pre-computed annotation data for genetic variants, organized by module: |
|
|
| | Module | Description | Files | |
| |--------|-------------|-------| |
| | longevitymap | Longevity-associated variants | annotations.parquet, studies.parquet, weights.parquet | |
|
|
| ## Schema |
|
|
| ### annotations.parquet |
| Variant-level facts linking rsIDs to genes and phenotypes. |
| - `rsid`: dbSNP reference ID |
| - `module`: Source module name |
| - `gene`: Associated gene symbol |
| - `phenotype`: Associated phenotype/trait |
| - `category`: Functional category |
|
|
| ### studies.parquet |
| Per-study evidence from scientific publications. |
| - `rsid`: dbSNP reference ID |
| - `module`: Source module name |
| - `pmid`: PubMed ID |
| - `population`: Study population |
| - `p_value`: Statistical significance |
| - `conclusion`: Study conclusion |
| - `study_design`: Type of study |
|
|
| ### weights.parquet |
| Curator-defined scoring for variant impact. |
| - `rsid`: dbSNP reference ID |
| - `genotype`: Genotype as list[str] (e.g., ["C", "T"]) |
| - `module`: Source module name |
| - `weight`: Numeric weight |
| - `state`: "protective", "risk", or "neutral" |
| - `priority`: Priority level |
| - `conclusion`: Curator conclusion |
| - `curator`: Curator name |
| - `method`: Curation method |
|
|
| ## Usage |
|
|
| ```python |
| import polars as pl |
| |
| # Load from HuggingFace |
| weights = pl.read_parquet("hf://datasets/just-dna-seq/annotators/data/longevitymap/weights.parquet") |
| studies = pl.read_parquet("hf://datasets/just-dna-seq/annotators/data/longevitymap/studies.parquet") |
| annotations = pl.read_parquet("hf://datasets/just-dna-seq/annotators/data/longevitymap/annotations.parquet") |
| ``` |
|
|
| ## Statistics |
|
|
| - **Modules**: 1 (longevitymap) |
| - **Total files**: 3 |
| - **Total size**: 0.09 MB |
|
|
| ## License |
|
|
| MIT License - See [LICENSE](LICENSE) for details. |
|
|
| ## Citation |
|
|
| If you use this data, please cite the original sources: |
| - LongevityMap: [https://longevitymap.org/](https://longevitymap.org/) |
|
|
