| --- |
| license: cc-by-4.0 |
| task_categories: |
| - tabular-regression |
| tags: |
| - biology |
| - oligonucleotides |
| - siRNA |
| - ASO |
| - shRNA |
| - HELM |
| configs: |
| - config_name: alharbi_2020_1 |
| data_files: |
| - split: train |
| path: alharbi_2020_1.csv.gz |
| - config_name: alharbi_2020_2 |
| data_files: |
| - split: train |
| path: alharbi_2020_2.csv.gz |
| - config_name: hagedorn_2022_1 |
| data_files: |
| - split: train |
| path: hagedorn_2022_1.csv.gz |
| - config_name: hwang_2024_1 |
| data_files: |
| - split: train |
| path: hwang_2024_1.csv.gz |
| - config_name: ichihara_2007_1 |
| data_files: |
| - split: train |
| path: ichihara_2007_1.csv.gz |
| - config_name: ichihara_2007_2 |
| data_files: |
| - split: train |
| path: ichihara_2007_2.csv.gz |
| - config_name: knott_2014_1 |
| data_files: |
| - split: train |
| path: knott_2014_1.csv.gz |
| - config_name: martinelli_2023_1 |
| data_files: |
| - split: train |
| path: martinelli_2023_1.csv.gz |
| - config_name: mcquisten_2007_1 |
| data_files: |
| - split: train |
| path: mcquisten_2007_1.csv.gz |
| - config_name: moe_neurotox_1 |
| data_files: |
| - split: train |
| path: moe_neurotox_1.csv.gz |
| - config_name: papargyri_2020_1 |
| data_files: |
| - split: train |
| path: papargyri_2020_1.csv.gz |
| - config_name: shmushkovich_2018_1 |
| data_files: |
| - split: train |
| path: shmushkovich_2018_1.csv.gz |
| - config_name: metadata |
| data_files: |
| - split: train |
| path: metadata.csv |
| --- |
| |
| # CollageBio Oligonucleotide Datasets |
|
|
| Curated benchmark datasets for oligonucleotide activity, toxicity, and |
| immunomodulation prediction. Each dataset is stored as a gzip-compressed |
| CSV with columns: |
|
|
| | Column | Description | |
| |---|---| |
| | `x` | HELM string for the oligonucleotide | |
| | `y` | Numeric label (activity / toxicity score) | |
| | `targets` | mRNA target identifier | |
|
|
| ## Datasets |
|
|
| | Key | Canonical Name | OligoGym ID | Modality | Collection | Samples | Source | |
| |---|---|---|---|---|---|---| |
| | `ichihara_2007_1` | Ichihara_2007_1 | Huesken | SIRNA | activity | 2,431 | [DOI](https://doi.org/10.1093/nar/gkm699) | |
| | `ichihara_2007_2` | Ichihara_2007_2 | Ichihara | SIRNA | activity | 419 | [DOI](https://doi.org/10.1093/nar/gkm699) | |
| | `alharbi_2020_1` | Alharbi_2020_1 | TLR7 | ASO | immunomodulation | 192 | [DOI](https://doi.org/10.1093/nar/gkaa523) | |
| | `alharbi_2020_2` | Alharbi_2020_2 | TLR8 | ASO | immunomodulation | 192 | [DOI](https://doi.org/10.1093/nar/gkaa523) | |
| | `hagedorn_2022_1` | Hagedorn_2022_1 | Neurotox LNA | ASO | toxicity | 1,825 | [DOI](https://doi.org/10.1089/nat.2021.0071) | |
| | `hwang_2024_1` | Hwang_2024_1 | ASOptimizer | ASO | activity | 32,602 | [DOI](https://doi.org/10.1016/j.omtn.2024.102186) | |
| | `knott_2014_1` | Knott_2014_1 | Sherwood | SHRNA | activity | 291,551 | [DOI](https://doi.org/10.1016/j.molcel.2014.10.025) | |
| | `moe_neurotox_1` | MOE_Neurotox_1 | Neurotox MOE | ASO | neurotoxicity | 2,437 | [DOI](https://patents.google.com/patent/WO2020172559A1) | |
| | `martinelli_2023_1` | Martinelli_2023_1 | siRNAmod | SIRNA | activity | 907 | [DOI](https://doi.org/10.1016/j.ygeno.2024.110815) | |
| | `mcquisten_2007_1` | McQuisten_2007_1 | OpenASO | ASO | activity | 3,913 | [DOI](https://doi.org/10.1186/1471-2105-8-184) | |
| | `papargyri_2020_1` | Papargyri_2020_1 | Cytotox LNA | ASO | toxicity | 768 | [DOI](https://doi.org/10.1016/j.omtn.2019.12.011) | |
| | `shmushkovich_2018_1` | Shmushkovich_2018_1 | Shmushkovich | SIRNA | activity | 356 | [DOI](https://doi.org/10.1093/nar/gky745) | |
|
|
| ## Usage |
|
|
| ```python |
| from datasets import load_dataset |
| |
| # Load a single dataset |
| ds = load_dataset("CollageBio/oligo-datasets", name="ichihara_2007_1") |
| df = ds["train"].to_pandas() |
| |
| # Or download the raw file directly |
| # https://huggingface.co/datasets/CollageBio/oligo-datasets/resolve/main/ichihara_2007_1.csv.gz |
| ``` |
|
|
