---
license: other
tags:
  - GRCh38
  - GRCm38
language:
  - en
  - zh
---
<p align="center">
  <strong>
    <span style="font-size: 30px;">AlphaGenome Dataset</span>
  </strong>
</p>

## Dataset Description

AlphaGenome Dataset is a curated package of reference genomes, annotation files, and TFRecord data for use with the OneScience AlphaGenome model.

The reference resources include human GRCh38.p13, mouse GRCm38.p6, FAI indexes, Gencode annotations, splice-site annotations, and polyA annotations. The TFRecord data contains 12 bundles from the HOMO_SAPIENS VALID split, with 25 gzip-compressed shards in each bundle.

## Supported Tasks

This dataset has been adapted for `OneScience-Group/alphagenome/`. By default, the model repository expects this dataset to be located at `data/alphagenome_dataset` within the model package. It is used for preflight checks, interval inference, variant scoring, and track-prediction evaluation.

## Dataset Format and Structure

TFRecord file paths follow this pattern:

```text
v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/<BUNDLE>/data_chrAll_01-25.gz.tfrecord
```

The bundles comprise ATAC, DNASE, PROCAP, CAGE, RNA_SEQ, CHIP_TF, CHIP_HISTONE, CONTACT_MAPS, SPLICE_SITES, SPLICE_SITE_USAGE, SPLICE_JUNCTIONS, and SPLICE_SITE_POSITIONS. Each sample contains a DNA sequence, interval chromosome/start/end metadata, a target tensor, and a mask; see `metadata/schema.yaml` for dtype and resolution.

## How to Use the Dataset

### Files and Download

Standalone download:

```bash
hf download --dataset OneScience-Group/alphagenome_dataset --local-dir .
```

Use within the model package:

```bash
hf download --dataset OneScience-Group/alphagenome_dataset --local-dir data/alphagenome_dataset
```

### Data Placement and Validation

When used as a model dependency, the following directory structure is recommended:

```text
<model-package>/data/alphagenome_dataset/
├── manifest.yaml
├── metadata/
├── reference/
└── v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
```

Quickly validate file presence, sizes, and gzip readability:

```bash
python scripts/validate_dataset.py --root .
```

Add `--check-sha256` to perform a complete SHA256 validation.

## Official OneScience Information

| Platform | OneScience Main Repository | Skills Repository |
|---|---|---|
| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |

## Limitations and License

license: mixed
license_note: >
  AlphaGenome training, validation and test datasets contain reprocessed
  data from FANTOM5, 4D Nucleome, ENCODE and GENCODE. Usage is subject
  to the respective source-specific licenses and data-use policies.
  Other unspecified materials are licensed under CC BY-NC 4.0.