ToxiVerse

Assay Profiler

This module provides a comprehensive workflow for chemical-assay profiling using bioassay data from PubChem to fill experimental data gaps. Users can upload up to 500 chemicals to profile them using PubChem bioassays.

Upload a file containing the CIDs of compounds you would like to profile based on assay outcomes. This should be a single-column txt or csv file containing the PubChem CID's of the compounds you wish to obtain HTS data for. Please check the sample files provided below. If you have compounds as another identifier (e.g., SMILES) PubChem offers a helpful batch-conversion tool located here.https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi

Download Sample CSV

Download Sample TXT

Upload Dataset File (Formats: .txt, .csv):

What Each Download Option Means

Download Bioprofile: Exports the bioprofile matrix with chemicals as rows and bioassays as columns. Activity values are encoded as 1 (Active/Probe), 0 (Inactive), and -1 (Inconclusive or Missing).
Download Heatmap: Provides a clustered heatmap visualization of the bioprofile matrix, helping identify patterns of activity across assays and compounds. Supports up to 2000 assay columns.
Download Model Metrics: Provides detailed performance statistics (Accuracy, Precision, Recall, F1-score, ROC AUC) for Random Forest models trained on the top informative assays.
Download Model Metrics Plot: Displays bar charts that visualize model performance, helping assess the reliability of each model.
Download Filled Data Gaps Matrix: Returns a chemical-assay matrix with missing activity values imputed using trained models from selected informative assays to fill experimental gaps.