| name | omg |
| description | Open MetaGenomic (OMG) corpus and gLM2 mixed-modality genomic language model — large pretraining data from IMG + MGnify (Tbp-scale DNA + billions of CDS). Use when: (1) Pretraining or evaluating genomic LMs, (2) Using gLM2 embeddings for function / coevolution / regulatory syntax, (3) Distinguishing ML corpora from study reanalysis. Hugging Face: tattabio/OMG, tattabio/gLM2_650M. Upstream: https://github.com/TattaBio/OMG. Route via genome-language-model.
|
| license | MIT |
| category | utilities |
| tags | ["OMG","gLM2","foundation-model","pretraining","HuggingFace"] |
| upstream | https://github.com/TattaBio/OMG |
OMG corpus / gLM2
Dataset: https://huggingface.co/datasets/tattabio/OMG ·
Model: https://huggingface.co/tattabio/gLM2_650M ·
Code: TattaBio/OMG
Citation
Cornman, A. et al. The OMG dataset: An Open MetaGenomic corpus for
mixed-modality genomic language modeling. bioRxiv
https://doi.org/10.1101/2024.08.14.607850 (2024).
See also docs/references.md and metagenomics-llm.
Analytical thinking
OMG aggregates and filters metagenomic sequence from JGI IMG and EMBL
MGnify into a mixed-modality corpus (amino acids for CDS, nucleic acids for
intergenic regions; ~3.1 Tbp + ~3.3B CDS in the preprint) for genomic language
modeling. gLM2 (Tatta Bio / Hwang et al.) uses genomic context for
functional representations and can capture cross-protein coevolutionary
signal better than single-protein ESM2 or short-context Evo-1 in the OMG/gLM2
analyses — still not a substitute for experimental contacts or classical
taxonomy.
| Use | Yes | No |
|---|
| Pretrain / fine-tune / embed with gLM2 | ✓ | |
| Replace MetaPhlAn/Kraken for your cohort | | ✗ |
| Cite as “we downloaded OMG instead of ENA runs” for a clinical study | | ✗ without justification |
Always separate ML corpus access from biological sample reanalysis
(sra-ena, mgnify analyses).
How to access
Pin dataset revision + model checkpoint in Methods. Expect large disk and GPU.
Decision tree
Need metagenome-scale LM resources?
├─ Pretrain corpus / gLM2 embeddings → omg
├─ DNA NT / DNABERT-2 / Caduceus / Evo 2 → genome-language-model
├─ Protein remote search only → plmsearch / deepblast
└─ Public study FASTQ → sra-ena / mgnify (not OMG)
Related skills
genome-language-model · metagenomics-llm · nucleotide-transformer ·
dnabert2 · caduceus · evo2 · mgnify · public-databases ·
plmsearch · spacedust · eggnog-mapper
