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add dataset card

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- add metadata fields (`license`, `tags`, `task_categories`, `size_categories`, `dataset_info`)
- add dataset description and composition details
- add example usage with `datasets.load_dataset`
- add citation for the Evo 2 preprint

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  1. README.md +78 -3
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- ---
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- license: apache-2.0
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- ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ ---
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+ license: apache-2.0
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+ tags:
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+ - biology
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+ - genomics
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+ - dna
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+ - foundation-models
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+ - arc-institute
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+ - evo2
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+ - science
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+ - huggingscience
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+ pretty_name: OpenGenome2
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+ task_categories:
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+ - text-generation
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+ - fill-mask
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+ - feature-extraction
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+ size_categories:
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+ - n>1T
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+ dataset_info:
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+ features:
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+ - name: text
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+ dtype: string
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+ splits:
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+ - name: train
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+ dataset_size: 880000000000
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+ ---
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+ # OpenGenome2
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+
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+ OpenGenome2 is a large-scale genomic dataset compiled by the Arc Institute and collaborators to train **Evo 2**, a biological foundation model.
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+ It contains **8.8 trillion nucleotides** from across the tree of life, including bacteria, archaea, eukaryotes, bacteriophage, organelles, and curated metagenomic assemblies.
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+
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+ Sequences are provided as text strings (A, T, C, G) at **single-nucleotide resolution**, optimized for training long-context genome language models.
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+
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+ ## Composition
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+
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+ - **Prokaryotes**: 113,379 representative genomes (~357B nt, GTDB v220.0)
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+ - **Eukaryotes**: 15,032 curated reference genomes (~6.98T nt, NCBI)
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+ - **Metagenomic assemblies**: 854B nt
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+ - **Organelle genomes**: 2.82B nt
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+ - **Eukaryotic augmentation**: 602B nt enriched for gene-rich regions
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+
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+ ⚠️ **Eukaryotic viral genomes are excluded** to mitigate dual-use concerns.
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+
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+ ## Dataset Features
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+
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+ | **Field** | **Type** | **Description** |
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+ |-----------|----------|-----------------|
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+ | `text` | string | Raw nucleotide sequence (can be millions of bp long) |
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+
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+ ## Example Usage
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+
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+ ```python
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+ from datasets import load_dataset
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+ # Load in streaming mode
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+ ds = load_dataset("arcinstitute/opengenome2", split="train", streaming=True)
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+ # Inspect first example
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+ example = next(iter(ds))
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+ print(len(example["text"]))
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+ print(example["text"][:100]) # first 100 bp
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+ ```
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+
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+ ## Citation
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+ Please cite the following when using OpenGenome2:
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+ ```
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+ @article {Brixi2025.02.18.638918,
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+ author = {Brixi, Garyk and Durrant, Matthew G and Ku, Jerome and Poli, Michael and Brockman, Greg and Chang, Daniel and Gonzalez, Gabriel A and King, Samuel H and Li, David B and Merchant, Aditi T and Naghipourfar, Mohsen and Nguyen, Eric and Ricci-Tam, Chiara and Romero, David W and Sun, Gwanggyu and Taghibakshi, Ali and Vorontsov, Anton and Yang, Brandon and Deng, Myra and Gorton, Liv and Nguyen, Nam and Wang, Nicholas K and Adams, Etowah and Baccus, Stephen A and Dillmann, Steven and Ermon, Stefano and Guo, Daniel and Ilango, Rajesh and Janik, Ken and Lu, Amy X and Mehta, Reshma and Mofrad, Mohammad R.K. and Ng, Madelena Y and Pannu, Jaspreet and Re, Christopher and Schmok, Jonathan C and St. John, John and Sullivan, Jeremy and Zhu, Kevin and Zynda, Greg and Balsam, Daniel and Collison, Patrick and Costa, Anthony B. and Hernandez-Boussard, Tina and Ho, Eric and Liu, Ming-Yu and McGrath, Tom and Powell, Kimberly and Burke, Dave P. and Goodarzi, Hani and Hsu, Patrick D and Hie, Brian},
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+ title = {Genome modeling and design across all domains of life with Evo 2},
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+ elocation-id = {2025.02.18.638918},
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+ year = {2025},
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+ doi = {10.1101/2025.02.18.638918},
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+ publisher = {Cold Spring Harbor Laboratory},
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+ URL = {https://www.biorxiv.org/content/early/2025/02/21/2025.02.18.638918},
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+ eprint = {https://www.biorxiv.org/content/early/2025/02/21/2025.02.18.638918.full.pdf},
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+ journal = {bioRxiv}
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+ }
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+ ```
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+
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+ ---