1. The CompTox Chemistry Dashboard: an informational data hub at the
National Center for Computational Toxicology
1Antony Williams*, 1Chris Grulke, 1Jennifer Smith, 2Kamel Mansouri, 2Andrew McEachran, 1Grace Patlewicz,
2Jeremy Fitzpatrick, 1Ann Richard, and 1Jeff Edwards
1U.S. EPA, National Center for Computational Toxicology (NCCT), Research Triangle Park, NC, 2Oak Ridge Institute for Science and Education
(ORISE) Participant, Research Triangle Park, NC,
ACS Meeting,
San Francisco
April 2-6, 2017
ORCID:
Antony Williams l l
Problem Definition and Goals
Accessing ~10 Million Predicted Properties Online
The CompTox Chemistry Dashboard
Problem: There is limited access online to freely available data to support computational toxicology in environmental science.
Goals: To deliver online access via a simple to use web-based interface supporting diverse types of data associated with environmental chemistry, and specifically computational toxicology. To develop predictive models from the data and use these models to predict properties for the ca. 750,000 chemicals within the database and make the predicted values available. To provide details regarding the performance of the models. To make the data available as downloadable Open data.
The dashboard provides access to ~750,000 chemicals from EPA’s DSSTox database [1]. It integrates curated experimental data [2] used to produce our “OPERA” models. All chemicals were passed through the prediction models and detailed model reports showing global and local applicability domains and nearest neighbor results are displayed in the application. The QSAR Modeling Report Formats (QMRF) for each model are available for each predicted endpoint.
The landing page of the dashboard is a simple text entry box allowing a type-ahead search for systematic, trade and trivial names, CAS Registry Numbers and InChIs.
Dashboard Entry Page
Where possible, links are provided to related Wikipedia articles. An associated mol file is available for download to the desktop, and a summary report containing record data can be provided as a PDF file.
Abstract
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. Much has been learned from the development of a disparate suite of software applications and recent work has focused on the integration of the various data sources into a new software architecture. This architecture is intended to reduce the learning curve for multiple applications, uses curated data sources to improve data integration and recall, and ultimately delivers better data in a more consumable form for both the user visiting a website and to computers visiting web services. The resulting application is the CompTox Chemistry dashboard. This application provides access to ~750,000 chemicals and associated experimental and predicted properties, high-throughput screening data from the ToxCast project, and product and functional use data. Flexible searching supports simple chemical identifier look-up based on chemical name and CAS registry number (CASRN) and structure identification is feasible using mass and formula based searching to support mass spectrometrists performing non-targeted analysis. Batch-based searching provides the user with the ability to look up large collections of chemical data using inputs based on name, CASRN, InChI keys and other identifiers and to export associated information in a series of standard file formats. The CompTox Chemistry Dashboard architecture and development approach has delivered a foundation on which to build new applications for use within the Agency and for use by the research community. This poster reviews the available types of data and the present capabilities and functionality of the CompTox Chemistry Dashboard.
Chemical Record Page: Atrazine
A summary of available chemical properties for Bisphenol A
The model report for the melting point prediction for Bisphenol A – including nearest neighbors.
For records with chemical structure representations, various inherent properties (e.g. formula and mass) and predicted physicochemical properties (logP, water solubility etc.) are provided.
Future Work
Continue to expand the data in terms of chemicals, toxicity data, additional experimental data
Release NCCT models as interactive online prediction tools in the near future via the dashboard.
Integrate the suite of EPA T.E.S.T3 physicochemical and toxicity prediction models to expand the collection of available models.
Add additional functionality supporting the display of bioassay data.
Chemical Properties Panel
The Toxicity Values tab provides access to data assembled from a series of public resources including EPA data (i.e. IRIS and PPRTV reports, ToxRef DB). Data can be downloaded as TSV and Excel files.
References
EPA Distributed Structure-Searchable Toxicity (DSSTox) Database,
Mansouri et al. An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling, SAR QSAR Environ Res Nov;27(11):
EPA Toxicity Estimation Software Tool (T.E.S.T.) software
Toxicity Values Panel
Literature searching using integration to a series of online resources can be performed using the CASRN and chemical name. This includes Google Scholar, PubMed and PubChem patents.
Future Work
The authors would like to acknowledge specific colleagues within our center for their contributions to the development of the dashboard: Nancy Baker, Richard Judson, Sean Watford and John Wambaugh.
Literature: Pubmed Abstract Sifter
This presentation does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.