yhao-compbio / tox_data

Collect datasets for computational toxicology

This aim of this repository is to collect and process toxicological datasets.

OFFSIDES: drug-adverse event relationships

The table below shows some basic summary statistics of OFFSIDES data.

Number of adverse events	1,227
Numbler or drugs invovled	2,728
Average number of samples per adverse event	912
Average number of positive samples per adverse event	171
Average number of negative samples per adverse event	741

Tox21: toxicity assay screen for environmental chemicals and approved drugs

Detailed documentation about the source dataset can be found at downloads/. Detailed documentation about the code can be found at src/. Detailed documentation about the generated dataset can be found at data/.

References

• Tatonetti NP, Patrick PY, Daneshjou R, Altman RB. Data-driven prediction of drug effects and interactions. Science translational medicine. 2012 Mar 14;4(125):125ra31-.

• Huang R. A Quantitative High-Throughput Screening Data Analysis Pipeline for Activity Profiling. In: Zhu H, Xia M, editors. High-Throughput Screening Assays in Toxicology. Methods in Molecular Biology. 1473. 1 ed: Humana Press; 2016

• Huang R, Xia M, Sakamuru S, Zhao J, Shahane SA, Attene-Ramos M, Zhao T, Austin CP, Simeonov A. (2016) Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization. Nat Commun. 7:10425

• Huang R, Xia M, Sakamuru S, Zhao J, Lynch C, Zhao T, Zhu H, Austin CP, Simeonov A. (2018) Expanding biological space coverage enhances the prediction of drug adverse effects in human using in vitro activity profiles. Sci Rep. 8(1):3783

• Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL. A next generation connectivity map: L1000 platform and the first 1,000,000 profiles. Cell. 2017 Nov 30;171(6):1437-52