metadata

license: mit
tags:
  - biology
configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train-*
dataset_info:
  features:
    - name: counts
      sequence: int32
    - name: counts_norm
      sequence: float32
    - name: counts_log
      sequence: float32
    - name: counts_log_norm
      sequence: float32
    - name: gene_names
      sequence: string
    - name: control_counts
      sequence: float32
    - name: control_counts_norm
      sequence: float32
    - name: control_counts_log
      sequence: float32
    - name: control_counts_log_norm
      sequence: float32
    - name: delta_counts
      sequence: float32
    - name: delta_counts_norm
      sequence: float32
    - name: delta_counts_log
      sequence: float32
    - name: delta_counts_log_norm
      sequence: float32
    - name: cell_line
      dtype: string
    - name: perturbation
      dtype: string
    - name: compound_concentration
      dtype: float64
    - name: compound_unit
      dtype: string
    - name: compound_smiles
      dtype: string
    - name: mechanism
      dtype: string
    - name: moa
      dtype: string
    - name: biological_effect
      dtype: string
    - name: experimental_id
      dtype: string
    - name: timepoint
      dtype: string
    - name: text
      dtype: string
    - name: text_embeddings
      sequence: float32
    - name: chembert_embeddings
      sequence: float32
  splits:
    - name: train
      num_bytes: 176083286910
      num_examples: 49392
  download_size: 65016664023
  dataset_size: 176083286910

I AM NOT AFFILIATED WITH NOVARTIS IN ANY WAY; THIS IS SIMPLY AN UPLOAD OF THEIR DATASET, "NOVARTIS/DRUG-SEQ U2OS MOABOX DATASET."

Novartis DRUG-seq U2OS MoABox Dataset

This dataset profiles transcriptomic responses of the U-2 OS human osteosarcoma cell line to a broad collection of small molecule perturbations. It contains 49,392 observations spanning 3,742 unique compounds tested at 4 distinct dosages + 0.0, each annotated with their respective mechanisms of action (MoA).

Each observation records gene expression data for 59,594 genes.

The dataset was generated using the DRUG-seq platform, enabling high-throughput, unbiased transcriptomic readouts suited for drug discovery applications.

Additional Information

Perturbation dosages range across 4 unique concentration values + 0.0.
Observations include multiple experimental replicates and plate layouts.
Normalized counts were scaled so that the total expression per cell sums to 1e4.
Control counts represent the average expression of each gene across all control cells.
Delta values are computed as the difference between each sample's expression and the corresponding control mean.
SMILES strings and mechanism of action (MoA) annotations curated by Novartis, retrieved from the ChEMBL database and enhanced with additional sources.

Citations

Hadjikyriacou, A., Yang, C., Henault, M., et al.
Novartis DRUG-seq U2OS MoABox Dataset
Novartis DRUG-seq GitHub Repository

Hadjikyriacou, A., Yang, C., Henault, M., Ge, R., Mansur, L., Lindeman, A., Russ, C., Renner, S., Hild, M., Jenkins, J., Gubser-Keller, C., Li, J., Ho, D. J., Neri, M., Sigoillot, F. D., & Ihry, R. (2025).
Novartis/DRUG-seq U2OS MoABox Dataset (1.0.0) [Data set]. Zenodo.
https://doi.org/10.5281/zenodo.14291446

Li, J., Ho, D. J., Henault, M., Yang, C., Neri, M., Ge, R., Renner, S., Mansur, L., Lindeman, A., Tumkaya, T., Russ, C., Hild, M., Gubser Keller, C., Jenkins, J. L., Worringer, K. A., Sigoillot, F. D., & Ihry, R. J. (2021).
DRUG-seq Provides Unbiased Biological Activity Readouts for Drug Discovery. bioRxiv.
https://doi.org/10.1101/2021.06.07.447456
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