Comptox Tools and Resources

The Tox21 Toolbox contains data-analysis tools for accessing and visualizing Tox21 quantitative high-throughput screening (qHTS) 10K library data, as well as integrating with other publicly available data.

NIEHS/DTT CompTox Tools and Resources

• Data Analysis tools facilitate the analysis and visualization of Tox21 data.
  • BMDExpress 2 and BMDExpress 3 allow users to perform genomic dose-response analyses, with the goal of identifying gene set/pathway-level potency estimates.
  • CurveP is software that employs a non-parametric approach and noise filtering for modeling high throughput dose-response data.
  • OPERA Open (Quantitative) Structure-activity/property Relationship App (OPERA) was created to provide robust QSAR/QSPR models for chemical properties of environmental interest that can be used for regulatory purposes. OPERA is a free and open-source/open-data suite of QSAR models providing predictions for physicochemical properties, environmental fate parameters, and toxicity endpoints. All OPERA models were built on curated data and QSAR-ready chemical structures standardized using an open-source workflow.
• Data Visualization tools provide quick, easy-to-use Tox21 qHTS data access, visualization, and clustering.
  • Tox21 Curve Browser (beta version) lets users visualize the concentration-response curves of compounds of interest, with the ability to superimpose assay results per compound for easy comparison.
  • Tox21 Activity Profiler (beta version) lets users prioritize compounds through compound structure and/or Tox21 qHTS data activity clustering visualization. Plots and data are available for download.
  • Tox21 Correlation Browser allows the user to select a chemical in Tox21 and search the rest of Tox21 chemicals based either on the biological fingerprint as defined by different potency and efficacy metrics across Tox21 assays or by chemical structure fingerprint (i.e., structural similarity).
  • Developmental NeuroToxicity Data Integration and Visualization Enabling Resource (DNT-DIVER) to analyze, compare, and visualize multiple DNT assays in an interactive web-application.
• Data Integration applications integrate data from external resources to facilitate interpretation of Tox21 data.
  • Tox21 Enricher (beta version) allows users to upload a set of compounds and find enriched toxicological characteristics from biological data sources such as DrugMatrix, PubChem, Comparative Toxicogenomics Database, and Leadscope.
  • Tox21 IVIVE Dose Equivalent (beta version) provides dose estimates for the likelihood of in vivo human biological interactions, using Tox21 data and high-throughput toxicokinetics modeling.
  • Integrated Chemical Environment (ICE) provides curated data from NICEATM, its partners, and other resources, as well as tools to facilitate the safety assessment of chemicals.
  • Tox21 BodyMap provides a visualization of mapping 971 Tox21/ToxCast assay targets to regions of the human body, and allows users to identify target tissues where a specific chemical is more likely to produce effects.
• Data
  • Chemical Effects in Biological Systems (CEBS) database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial, and governmental laboratories. Data in CEBS are housed in a relational database designed to display data in the context of biology and study design, and permit data integration for cross-study analysis, knowledge generation and novel meta analysis.
  • DrugMatrix is a large integrated rat toxicogenomics data set that can be used for modelling relationships between high throughput and guideline toxicology endpoints (e.g., pathology).
  • Tox21 Database API is a deeply annotated resource for Tox21 high throughput screening data.

External Tools

• PubChem provides access to large-scale screening data (including, but not limited to, Tox21 qHTS data). This tool also allows access to the medicinal chemistry and informatics necessary to identify chemical probes that study the functions of genes, cells, and biochemical pathways. PubChem is organized as three linked databases—PubChem Substance, PubChem Compound, and PubChem BioAssay—within NCBI's Entrez information retrieval system.
• EPA hosts a collection of flat files for Tox21 and ToxCast programs as well as the EPA iCSS Dashboard. These include assay and chemical descriptions, HTS data, and other related files.