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README.md

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-license: apache-2.0
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+---
+license: apache-2.0
+pretty_name: OpenGenome2
+tags:
+  - huggingscience
+  - science
+  - biology
+  - genomics
+  - dna
+  - sequence-modeling
+  - long-context
+  - metagenomics
+  - microbiology
+  - bacteriophage
+  - plasmid
+  - mrna
+  - promoter
+  - ncrna
+  - organelle-genomes
+  - gtdb
+  - imgvr
+  - imgpr
+  - ncbi
+  - json
+  - fasta
+---
+
+# OpenGenome2
+
+OpenGenome2 is a large-scale, diverse DNA corpus spanning prokaryotes (bacteria & archaea), eukaryotes, organelles, bacteriophages, plasmids, and metagenomes. It was assembled to train long-context genomic foundation models (e.g., Evo 2) and emphasizes **functionally informative regions** (e.g., genic windows, promoters, noncoding RNAs) while providing comprehensive whole-genome coverage across the tree of life.
+
+* **License:** Apache-2.0
+* **Scope:** trillions of nucleotides aggregated across multiple public sources (e.g., GTDB v220, IMG/VR, IMG/PR, NCBI eukaryotic references) with curation and quality filtering to support genome-scale modeling.
+* **Formats:** JSONL (token-ready sequences) and FASTA (raw sequences).
+* **Splits:** `train`, `validation`, `test` are provided for most JSONL subsets.
+
+## Contents & Source Mapping
+
+The on-hub layout mirrors data provenance and training phase:
+
+* **`json/pretraining_or_both_phases/`**
+  Functional and broad-coverage sources used during pretraining (or used in both pre- and mid-training):
+
+  * `eukaryotic_genic_windows/` – windows enriched for coding/genic content
+  * `gtdb_v220_imgpr/` – prokaryotes from **GTDB v220** plus curated plasmids/phages from **IMG/PR**
+  * `imgvr_untagged/` – bacteriophage sequences from **IMG/VR**
+  * `metagenomes/` – metagenomic contigs
+  * `mrna/`, `mrna_splice_promoter/` – mRNA and splicing/promoter-focused windows
+  * `ncrna/` – noncoding RNAs
+  * `organelle/` – organellar genomes
+  * `promoters/` – promoter regions
+* **`json/midtraining_specific/`**
+  Additional curated data emphasized during mid-training:
+
+  * `gtdb_v220_stitched/` – stitched windows / references from **GTDB v220**
+  * `imgpr/` – curated plasmids & phages from **IMG/PR**
+  * `ncbi_eukaryotic_genomes/` – curated eukaryotic references from **NCBI**
+* **`fasta/`** mirrors these sources for users preferring raw FASTA (e.g., `fasta/gtdb_v220`, `fasta/mrna`, `fasta/organelles`, `fasta/promoters`, etc.).
+
+## Recommended Uses
+
+* Pretraining/continued-pretraining **DNA language models** (autoregressive or masked).
+* Long-context modeling (100 kbp–1 Mbp) for **regulatory architecture** and genome context tasks.
+* Zero-shot **variant effect** predictions on promoters/genic windows.
+* Embedding-based **functional clustering** across genomes, plasmids, and phages.
+* Generative modeling for **protein–DNA/RNA system design** when coupled with appropriate safety review.
+
+## Citation
+
+If you use OpenGenome2 or models trained on it, please cite:
+
+* **Evo 2** (trained on OpenGenome2):
+  Brixi *et al.*, “Genome modeling and design across all domains of life with Evo 2,” *bioRxiv* (2025).
+  [https://doi.org/10.1101/2025.02.18.638918](https://doi.org/10.1101/2025.02.18.638918)
+
+* **Data sources**:
+
+  * GTDB updated references (v220)
+  * IMG/VR (bacteriophages) and IMG/PR (plasmids/phages)
+  * NCBI eukaryotic genomes/references
+
+## Attribution
+
+* Dataset maintained by the **Arc Institute**. See the Hub repo for updates and discussions.