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Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System

Computational toxicology combines data from high-throughput test methods, chemical structure analyses and other biological domains (e.g., genes, proteins, cells, tissues) with the goals of predicting and understanding the underlying mechanistic causes of chemical toxicity and for predicting toxicity...

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Detalles Bibliográficos
Autores principales: Judson, Richard S., Martin, Matthew T., Egeghy, Peter, Gangwal, Sumit, Reif, David M., Kothiya, Parth, Wolf, Maritja, Cathey, Tommy, Transue, Thomas, Smith, Doris, Vail, James, Frame, Alicia, Mosher, Shad, Cohen Hubal, Elaine A., Richard, Ann M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291995/
https://www.ncbi.nlm.nih.gov/pubmed/22408426
http://dx.doi.org/10.3390/ijms13021805
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author Judson, Richard S.
Martin, Matthew T.
Egeghy, Peter
Gangwal, Sumit
Reif, David M.
Kothiya, Parth
Wolf, Maritja
Cathey, Tommy
Transue, Thomas
Smith, Doris
Vail, James
Frame, Alicia
Mosher, Shad
Cohen Hubal, Elaine A.
Richard, Ann M.
author_facet Judson, Richard S.
Martin, Matthew T.
Egeghy, Peter
Gangwal, Sumit
Reif, David M.
Kothiya, Parth
Wolf, Maritja
Cathey, Tommy
Transue, Thomas
Smith, Doris
Vail, James
Frame, Alicia
Mosher, Shad
Cohen Hubal, Elaine A.
Richard, Ann M.
author_sort Judson, Richard S.
collection PubMed
description Computational toxicology combines data from high-throughput test methods, chemical structure analyses and other biological domains (e.g., genes, proteins, cells, tissues) with the goals of predicting and understanding the underlying mechanistic causes of chemical toxicity and for predicting toxicity of new chemicals and products. A key feature of such approaches is their reliance on knowledge extracted from large collections of data and data sets in computable formats. The U.S. Environmental Protection Agency (EPA) has developed a large data resource called ACToR (Aggregated Computational Toxicology Resource) to support these data-intensive efforts. ACToR comprises four main repositories: core ACToR (chemical identifiers and structures, and summary data on hazard, exposure, use, and other domains), ToxRefDB (Toxicity Reference Database, a compilation of detailed in vivo toxicity data from guideline studies), ExpoCastDB (detailed human exposure data from observational studies of selected chemicals), and ToxCastDB (data from high-throughput screening programs, including links to underlying biological information related to genes and pathways). The EPA DSSTox (Distributed Structure-Searchable Toxicity) program provides expert-reviewed chemical structures and associated information for these and other high-interest public inventories. Overall, the ACToR system contains information on about 400,000 chemicals from 1100 different sources. The entire system is built using open source tools and is freely available to download. This review describes the organization of the data repository and provides selected examples of use cases.
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spelling pubmed-32919952012-03-09 Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System Judson, Richard S. Martin, Matthew T. Egeghy, Peter Gangwal, Sumit Reif, David M. Kothiya, Parth Wolf, Maritja Cathey, Tommy Transue, Thomas Smith, Doris Vail, James Frame, Alicia Mosher, Shad Cohen Hubal, Elaine A. Richard, Ann M. Int J Mol Sci Review Computational toxicology combines data from high-throughput test methods, chemical structure analyses and other biological domains (e.g., genes, proteins, cells, tissues) with the goals of predicting and understanding the underlying mechanistic causes of chemical toxicity and for predicting toxicity of new chemicals and products. A key feature of such approaches is their reliance on knowledge extracted from large collections of data and data sets in computable formats. The U.S. Environmental Protection Agency (EPA) has developed a large data resource called ACToR (Aggregated Computational Toxicology Resource) to support these data-intensive efforts. ACToR comprises four main repositories: core ACToR (chemical identifiers and structures, and summary data on hazard, exposure, use, and other domains), ToxRefDB (Toxicity Reference Database, a compilation of detailed in vivo toxicity data from guideline studies), ExpoCastDB (detailed human exposure data from observational studies of selected chemicals), and ToxCastDB (data from high-throughput screening programs, including links to underlying biological information related to genes and pathways). The EPA DSSTox (Distributed Structure-Searchable Toxicity) program provides expert-reviewed chemical structures and associated information for these and other high-interest public inventories. Overall, the ACToR system contains information on about 400,000 chemicals from 1100 different sources. The entire system is built using open source tools and is freely available to download. This review describes the organization of the data repository and provides selected examples of use cases. Molecular Diversity Preservation International (MDPI) 2012-02-09 /pmc/articles/PMC3291995/ /pubmed/22408426 http://dx.doi.org/10.3390/ijms13021805 Text en © 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Review
Judson, Richard S.
Martin, Matthew T.
Egeghy, Peter
Gangwal, Sumit
Reif, David M.
Kothiya, Parth
Wolf, Maritja
Cathey, Tommy
Transue, Thomas
Smith, Doris
Vail, James
Frame, Alicia
Mosher, Shad
Cohen Hubal, Elaine A.
Richard, Ann M.
Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System
title Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System
title_full Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System
title_fullStr Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System
title_full_unstemmed Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System
title_short Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System
title_sort aggregating data for computational toxicology applications: the u.s. environmental protection agency (epa) aggregated computational toxicology resource (actor) system
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291995/
https://www.ncbi.nlm.nih.gov/pubmed/22408426
http://dx.doi.org/10.3390/ijms13021805
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