README.md

metadata

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
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	neurotoxicity	2,437	DOI
martinelli_2023_1	Martinelli_2023_1	siRNAmod	SIRNA	activity	907	DOI
mcquisten_2007_1	McQuisten_2007_1	OpenASO	ASO	activity	3,913	DOI
papargyri_2020_1	Papargyri_2020_1	Cytotox LNA	ASO	toxicity	768	DOI
shmushkovich_2018_1	Shmushkovich_2018_1	Shmushkovich	SIRNA	activity	356	DOI

Usage

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