README.md

metadata

license: cc-by-4.0
task_categories:
  - tabular-regression
tags:
  - biology
  - oligonucleotides
  - siRNA
  - ASO
  - shRNA
  - HELM
  - oligogym
configs:
  - 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: 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: knott_2014_1
    data_files:
      - split: train
        path: knott_2014_1.csv.gz
  - config_name: moe_neurotox_1
    data_files:
      - split: train
        path: moe_neurotox_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: 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

OligoGym Datasets

A mirror of the 12 curated benchmark datasets shipped with OligoGym (Roche), repackaged as HuggingFace configs for convenient loading. Covers oligonucleotide activity, toxicity, and immunomodulation across ASO, siRNA, and shRNA modalities.

This is not a new dataset. Row counts, column sets, and values are identical to the files in OligoGym's oligogym/resources/pkg_dataset/. All credit for curation belongs to the OligoGym authors — please cite them (see Citation) and each dataset's own primary source.

Columns

Column	Description
x	HELM string for the oligonucleotide
y	Numeric label, as processed by OligoGym (the modelling target)
y_raw	Original label before clipping / scaling — differs from y for hwang_2024_1, knott_2014_1, moe_neurotox_1, papargyri_2020_1
targets	mRNA target identifier
smiles	SMILES representation
fasta	Nucleotide sequence

hwang_2024_1 additionally carries cell_line and concentration.

Datasets

Key	Canonical Name	OligoGym ID	Modality	Collection	Samples	Source(s)
ichihara_2007_1	Ichihara_2007_1	Huesken	SIRNA	activity	2,431	DOI
ichihara_2007_2	Ichihara_2007_2	Ichihara	SIRNA	activity	419	DOI
alharbi_2020_1	Alharbi_2020_1	TLR7	ASO	immunomodulation	192	DOI
alharbi_2020_2	Alharbi_2020_2	TLR8	ASO	immunomodulation	192	DOI
hagedorn_2022_1	Hagedorn_2022_1	Neurotox LNA	ASO	toxicity	1,825	DOI
hwang_2024_1	Hwang_2024_1	ASOptimizer	ASO	activity	32,602	DOI
knott_2014_1	Knott_2014_1	Sherwood	SHRNA	activity	291,551	DOI
moe_neurotox_1	MOE_Neurotox_1	Neurotox MOE	ASO	acute neurotoxicity	2,437	1 2 3 4 5 6 7 8 9 10 11 12 13
martinelli_2023_1	Martinelli_2023_1	siRNAmod	SIRNA	activity	907	DOI
mcquisten_2007_1	McQuisten_2007_1	OpenASO	ASO	activity	3,913	1 2
papargyri_2020_1	Papargyri_2020_1	Cytotox LNA	ASO	toxicity	768	DOI
shmushkovich_2018_1	Shmushkovich_2018_1	Shmushkovich	SIRNA	activity	356	DOI

moe_neurotox_1 is compiled from 13 separate WO (PCT) patent publications; mcquisten_2007_1 from a publication plus the openASO repository. All sources are linked above.

Usage

from datasets import load_dataset

# Load a single dataset
ds = load_dataset("CollageBio/oligogym", name="ichihara_2007_1")
df = ds["train"].to_pandas()

# Or download the raw file directly
# https://huggingface.co/datasets/CollageBio/oligogym/resolve/main/ichihara_2007_1.csv.gz

Citation

If you use these datasets, please cite the OligoGym paper:

@article{rotrattanadumrong2026oligogym,
  title={OligoGym: Curated Datasets and Benchmarks for Oligonucleotide Drug Discovery},
  author={Rotrattanadumrong, Rachapun and De Donno, Carlo},
  journal={Advances in Neural Information Processing Systems},
  volume={38},
  year={2026}
}

Upstream code and original data: https://github.com/Roche/OligoGym