File size: 3,275 Bytes
dbb944f 5f82e5e 00b49d9 5f82e5e 00b49d9 5f82e5e |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 |
---
dataset_info:
features:
- name: CDS_position_ids
sequence: int32
- name: IGS_position_ids
sequence: int32
- name: CDS_ids
sequence: string
- name: IGS_ids
sequence: string
- name: CDS_seqs
sequence: large_string
- name: IGS_seqs
sequence: large_string
- name: CDS_orientations
sequence: bool
splits:
- name: train
num_bytes: 1916402470934
num_examples: 270640482
download_size: 1253813127320
dataset_size: 1916402470934
configs:
- config_name: default
data_files:
- split: train
path: data/train-*
---
# OMG: An Open MetaGenomic Dataset
The OMG is a 3.1T base pair metagenomic pretraining dataset, combining EMBL's MGnify and JGI's IMG databases. The combined data is pre-processed into a mixed-modality dataset, with translated amino acids for protein coding sequences, and nucleic acids for intergenic sequences.
We make two additional datasets available on the HuggingFace Hub:
- [`OG`](https://huggingface.co/datasets/tattabio/OG): A subset of OMG consisting of high quality genomes with taxonomic information.
- [`OMG_prot50`](https://huggingface.co/datasets/tattabio/OMG_prot50): A protein-only dataset generated by clustering OMG at 50% sequence identity, resulting in 207M protein sequences.
See [https://github.com/TattaBio/OMG](https://github.com/TattaBio/OMG) for details and example tokenization script.
## Use
```python
import datasets
ds = datasets.load_dataset('tattabio/OMG')
```
To preview the dataset without downloading, load in streaming mode:
```python
import datasets
ds = datasets.load_dataset('tattabio/OMG', streaming=True)['train']
print(next(iter(ds)))
```
## Format
Each row of the dataset represents a genomic scaffold, as an ordered list of amino acid coding sequences (CDS) and nucleotide intergenic sequences (IGS).
| Feature | Description | Example |
|---|---|---|
| `CDS_seqs` | A list of strings representing the amino acid CDS sequences. | `['MALTKVEKRNR...', 'MLGIDNIERVK...', 'MATIKVKQVR...', 'MNLSNIKPAS...']` |
| `IGS_seqs` | A list of strings representing the nucleotide IGS sequences. | `['AATTTAAGGAA', 'TTTTAAAAGTATCGAAAT', 'TTTTTAAAGAAAA']` |
| `CDS_position_ids` | A list of integers representing the position of each CDS element in the scaffold. | `[1, 3, 5, 6]` |
| `IGS_position_ids` | A list of integers representing the position of each IGS element in the scaffold. | `[0, 2, 4]` |
| `CDS_ids` | A list of string identifiers for each CDS element. | `['7000000126\|C1821366\|CDS\|gene_115413\|+\|84:437', '7000000126\|C1821366\|CDS\|gene_115414\|+\|456:977', '7000000126\|C1821366\|CDS\|gene_115415\|+\|991:1167', '7000000126\|C1821366\|CDS\|gene_115416\|+\|1168:1689']` |
| `IGS_ids` | A list of string identifiers for each IGS element. | `['7000000126\|C1821366\|IG\|IG_000001\|+\|73:83', '7000000126\|C1821366\|IG\|IG_000002\|+\|438:455', '7000000126\|C1821366\|IG\|IG_000003\|+\|978:990']` |
| `CDS_orientations` | A list of booleans indicating the orientation of each CDS. `True` represents the forward strand, and `False` represents the reverse strand. | `[True, True, True, False]` |
The format for the CDS and IGS id fields is: `sample_accession|contig_id|feature_type|gene_id|strand|start:end`
## Citation
**BibTeX:**
TODO
|