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ToxCast Data: Accessing ToxCast Data and Scenarios for Exploring Data

ToxCast data can be accessed, explored and used in different ways and for many different purposes. This page highlights examples of ways to access and explore the data.

R-Package TCPL Scenarios

I would like to export data from ToxCast and review it.

This example assumes that users are familiar with R and the tcpl R Package.

This example is geared towards users who would like to review the ToxCast data at a processing level prior to that available in the ToxCast Dashboard (Level 6).

This example is in development.

I would like to register new high-throughput screening data for in vitro db.

This example assumes that users are familiar with R and the tcpl R Package.

This example, available in the tcpl VignetteExit, explains how to register and upload new data into the tcpl database using a small subset of ToxCast data showing changes in intracellular cortisol hormone. The subset of data comes from an assay measuring steroidogenesis through cellular levels of multiple steroid hormones.

The tcpl package provides three functions for adding new data:

  1. tcplRegister to register a new assay or chemical ID
  2. tcplUpdate to change or add additional information for existing assay or chemical IDs, and
  3. tcplWriteLvl0 for loading data.

Before writing any data to the tcpl database, the user has to register the assay and chemical information.

See the tcpl VignetteExitfor further details.

I would like to process my own data using the tcpl pipeline.

This example assumes that users are familiar with R and the tcpl R Package and have registered their data (see previous example for details).

This example, available in the tcpl VignetteExit, explains how the data are processed through the levels of the pipeline for single-concentration and multiple-concentration screening.

All processing in the tcpl package occurs at the assay component or assay endpoint level. There is no capability within either screening paradigm to do any processing which combines data from multiple assay components or assay endpoints. Any combining of data must occur before or after the pipeline processing.

The processing is sequential, and every level of processing requires successful processing at the antecedent level. The processing requirements vary by screening paradigm and level. The Vignette includes the details, but in general, many of the processing steps require specific methods to accommodate different experimental designs or data processing approaches.

See the tcpl VignetteExitfor further details.

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ToxCast Data Relevant to EPA's Endocrine Disruptor Screening Program

Based on scientific advances, EPA intends to implement the use of high throughput screening assays and computational models to evaluate, and to a significant extent, screen chemicals.

  • Endocrine Disruptor Screening Program. The in vitro high throughput and computational model alternatives provide an accurate quantitative measure of specific endocrine receptor binding bioactivity and mechanisms that can serve as alternatives to the current Tier 1 estrogen receptor (ER) binding, ER transactivation (ERTA) and uterotrophic assays.
  • Prioritizing Chemicals for Potential Endocrine Disruption. EPA researchers have been developing new rapid methods that can quickly screen thousands of chemicals.
  • High-throughput Screening Data for Estrogen Receptor Model. Estrogen receptor model data from the manuscrpit titled Integrated Model of Chemical Perturbations of Biological Pathways Using 18 In Vitro High-Throughput Screening Assays for the Estrogen Receptor (Judson et al.) published in Toxicological Sciences.


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