---
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
```