| --- |
| 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. |
