suzuki-2001/multi-model-plant-genome-corpus

Dataset Card: Multi Model Plant Genome Corpus

This is a modified version of the Plant Multi-Species Genomes dataset created by InstaDeepAI, focusing on 11 major crop species with adaptive splitting based on genome sizes.

Dataset Summary

The Plant Multi-Species Genome dataset contains DNA sequences from 11 different plant species:

1. Arabidopsis (GCF_000001735.4_TAIR10.1)
2. Tomato (GCF_000188115.4_SL3.0)
3. Rice (GCF_001433935.1_IRGSP-1.0)
4. Soybean (GCF_000004515.6)
5. Sorghum (GCF_000003195.3)
6. Maize (GCF_902167145.1)
7. Tobacco (GCF_000715135.1)
8. Wheat (GCF_018294505.1)
9. Cabbage (GCF_000695525.1)
10. Foxtail millet (GCF_000263155.2)
11. Cucumber (GCF_000004075.3)

Each sequence is processed into chunks with configurable length and overlap. The dataset employs an adaptive splitting strategy where the validation and test set ratios are determined based on genome sizes to ensure balanced representation while maintaining efficiency.

Dataset Structure

Data Instances

Each instance contains:

{
    'sequence': 'ACGTACGT...', # DNA sequence string
    'description': 'Species and genome information',
    'start_pos': 0,  # Start position in the original sequence
    'end_pos': 1000  # End position in the original sequence
}

• sequence: A string containing the DNA sequence
• description: A string containing the species information and NCBI identifier
• start_pos: Integer indicating the start position in the original sequence
• end_pos: Integer indicating the end position in the original sequence

Data Splits

The dataset is split into train, validation, and test sets using an adaptive strategy:

• Very large genomes (>20% of total): 0.2% for validation and test
• Large genomes (10-20%): 0.5% for validation and test
• Medium genomes (5-10%): 1% for validation and test
• Small genomes (<5%): 2% for validation and test

The maximum combined size of validation and test sets is capped at 10% for each genome.

Dataset Creation

Source Data

The source genomes are from NCBI RefSeq database, accessed through the original Plant Multi-Species Genomes dataset by InstaDeepAI.

Preprocessing

• Sequences are cleaned to contain only A, T, C, G, and N
• Sequences are split into chunks with configurable length and overlap
• Adaptive splitting is applied based on genome sizes

Usage

pythonCopyfrom datasets import load_dataset

Default configuration (1000bp chunks)

dataset = load_dataset("suzuki-2001/multi-model-plant-genome-corpus")

Custom chunk length

dataset = load_dataset("suzuki-2001/multi-model-plant-genome-corpus", chunk_length=6000)

Limitations

The dataset is limited to 11 species compared to the original 48 species Sequence length is restricted by the chunking process The adaptive splitting strategy may result in different split sizes across species

Citation

Please cite both the original dataset and this modified version:

bibtexCopy@article{mendoza2023foundational,
  title={A Foundational Large Language Model for Edible Plant Genomes},
  author={Mendoza-Revilla, Javier and Trop, Evan and Gonzalez, Liam and Roller, Masa and Dalla-Torre, Hugo and de Almeida, Bernardo P and Richard, Guillaume and Caton, Jonathan and Lopez Carranza, Nicolas and Skwark, Marcin and others},
  journal={bioRxiv},
  pages={2023--10},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}

bibtexCopy@article{o2016reference,
  title={Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation},
  author={O'Leary, Nuala A and Wright, Mathew W and Brister, J Rodney and Ciufo, Stacy and Haddad, Diana and McVeigh, Rich and Rajput, Bhanu and Robbertse, Barbara and Smith-White, Brian and Ako-Adjei, Danso and others},
  journal={Nucleic acids research},
  volume={44},
  number={D1},
  pages={D733--D745},
  year={2016},
  publisher={Oxford University Press}
}

License

This dataset follows the same license as the original NCBI RefSeq data and the InstaDeepAI plant-multi-species-genomes dataset. For detailed terms, please refer to:

• NCBI Terms and Conditions
• InstaDeepAI/plant-multi-species-genomes License