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README.md

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+---
+license: cc-by-4.0
+task_categories:
+  - tabular-regression
+tags:
+  - biology
+  - oligonucleotides
+  - siRNA
+  - ASO
+  - shRNA
+  - HELM
+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
+
+---
+
+# 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
+```