| --- |
| 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 | |
|
|
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|
