Update longevitymap module
Browse files- README.md +85 -3
- data/longevitymap/annotations.parquet +3 -0
- data/longevitymap/studies.parquet +3 -0
- data/longevitymap/weights.parquet +3 -0
README.md
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license: mit
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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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data/longevitymap/annotations.parquet
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version https://git-lfs.github.com/spec/v1
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oid sha256:43955314797d2122e0a435e9c33aed8cb9ff66d21abb2c1c443887a5a27cd2c7
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size 6250
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data/longevitymap/studies.parquet
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version https://git-lfs.github.com/spec/v1
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oid sha256:5c82e19bcf165c097488398c37a797a6bf0f5fe2efa05a0cd2955f309c9d99c5
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size 82642
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data/longevitymap/weights.parquet
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version https://git-lfs.github.com/spec/v1
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oid sha256:94dc2f927935478b3730e7a30c2486e566811c15994ddabe41a17b9a1cd53319
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size 11789
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