Datasets:

OryzaOrg
/

OryzaSNPs

license: cc-by-4.0
task_categories:
  - tabular-classification
  - tabular-regression
language:
  - en
tags:
  - genomics
  - snp
  - genotype
  - phenotype
  - agriculture
  - rice
  - set-learning
pretty_name: OryzaSNPs
size_categories:
  - 1K<n<10K
configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train/data-*.arrow
      - split: test
        path: data/test/data-*.arrow
  - config_name: genomic
    data_files:
      - split: train
        path: genomic/data-*.arrow

OryzaSNPs

Description

OryzaSNPs is a dataset of SNP (Single Nucleotide Polymorphism) genotypes and associated phenotypic traits for Oryza species. The dataset is designed for machine learning, statistical genetics, and genotype–phenotype association studies.

Dataset Structure

Split: `train`/`test`

Each row corresponds to one individual (specimen).

genotype (int8, shape: 177650)
Encoded SNP genotypes across the genome
phenotypes (float32, shape: 19)
Quantitative or encoded categorical traits

Auxiliary: `snps`

Metadata describing each SNP (shared across all samples).

chrom: Chromosome identifier
pos: Normalized genomic position (scaled to [0, 1] within chromosome)
allele: Encoded allele information

Genotype Encoding

Each SNP genotype is encoded as an integer in the set:

Value	Meaning
-1	Missing genotype (no reliable call)
0	Homozygous reference allele
1	Heterozygous (one reference, one alternate allele)
2	Homozygous alternate allele