Bioprofiler

This module builds bioprofile for chemicals using PubChem bioactvity data and fill experimental gaps. You can upload up to 500 chemicals (by PubChem CID). Assays with at least one active compound are selected; mutual information identifies informative assays; then Random Forest models (trained on up to 500 actives and 500 inactives per informative assay) impute missing values.

Upload a file containing PubChem CIDs (one per line) to profile by bioactivity data. Accepted formats: .txt or .csv, single column. If you have other identifiers (e.g., SMILES), use PubChem’s batch converter: ID Exchange

Download Sample CSV Download Sample TXT
File must be a single column of CIDs. Empty lines are ignored.
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), -1 (Inactive), and 0 (Inconclusive/Unspecified/empty).
  • Download Heatmap: A clustered heatmap of the bioprofile matrix to spot activity patterns across assays and chemicals. Supports up to 2000 assay columns.
  • Download Model Metrics: Detailed performance statistics (accuracy, precision, recall, F1-score, ROC AUC) for Random Forest models on top informative assays.
  • Download Model Metrics Plot: Box plot summarizing model performance for quick comparison.
  • Download Complete Bioprofile: Returns the complete bioprofile matrix with missing bioactivity values imputed using trained models.
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