metadata
license: apache-2.0
Overview
This dataset consists of reference genomes for 10 species:
| Species | Assembly Accession |
|---|---|
| Arabidopsis thaliana | GCF_000001735.4_TAIR10.1 |
| Caenorhabditis elegans | GCF_000002985.6_WBcel235 |
| Danio rerio | GCF_000002035.6_GRCz11 |
| Drosophila melanogaster | GCF_000001215.4_Release_6_plus_ISO1_MT |
| Felis catus | GCF_018350175.1_F.catus_Fca126_mat1.0 |
| Gallus gallus | GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b |
| Gorilla gorilla | GCF_029281585.2_NHGRI_mGorGor1-v2.0_pri |
| Homo sapiens | GCF_000001405.40_GRCh38.p14 |
| Mus musculus | GCF_000001635.27_GRCm39 |
| Salmo trutta | GCF_901001165.1_fSalTru1.1 |
Each item in the dataset contains the following fields:
"sequence": datasets.Value("string"),
"species_label": datasets.ClassLabel() # See below
"description": datasets.Value("string"),
"start_pos": datasets.Value("int32"),
"end_pos": datasets.Value("int32"),
"fasta_url": datasets.Value("string")
The class labels are as follows:
| Class | Label |
|---|---|
'Homo_sapiens' |
0 |
'Mus_musculus' |
1 |
'Drosophila_melanogaster' |
2 |
'Danio_rerio' |
3 |
'Caenorhabditis_elegans' |
4 |
'Gallus_gallus' |
5 |
'Gorilla_gorilla' |
6 |
'Felis_catus' |
7 |
'Salmo_trutta' |
8 |
'Arabidopsis_thaliana' |
9 |
Usage
To use this dataset, set the chunk_length (length of each sequence, in base-pairs) and the overlap (amount each sequence overlaps, in base-pairs).
The dataset only contains a train split.
We recommend randomly splitting the dataset to create validation/test sets.
See below for example usage:
import datasets
max_length = 32_768
overlap = 0
dataset = datasets.load_dataset(
'yairschiff/ten_species',
split='train', # original dataset only has `train` split
chunk_length=max_length,
overlap=overlap,
trust_remote_code=True
)
train_validation_splits = dataset.train_test_split(
test_size=0.05, seed=42)
Acknowledgments
Code for dataset processing is derived from https://huggingface.co/datasets/InstaDeepAI/multi_species_genomes.