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just-dna-seq/annotators

Genomic Variant Annotators Curated genomic variant annotation modules from the 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… See the full description on the dataset page: https://huggingface.co/datasets/just-dna-seq/annotators.

sourceHugging Facemitupdated 1mo agoView on Hugging Face
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Genomic Variant Annotators

Curated genomic variant annotation modules from the DNA-seq project.

Overview

This dataset contains pre-computed annotation data for genetic variants, organized by module:

ModuleDescriptionFiles
longevitymapLongevity-associated variantsannotations.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 for details.

Citation

If you use this data, please cite the original sources: