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Python BMDS: A Python interface library and web application for the canonical EPA dose-response modeling software.

Authors
  • Pham, Ly Ly1
  • Watford, Sean1
  • Friedman, Katie Paul1
  • Wignall, Jessica2
  • Shapiro, Andrew J3
  • 1 National Center for Computational Toxicology, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC USA. , (United States)
  • 2 ICF, Burlington, Vermont, USA.
  • 3 National Toxicology Program at NIEHS, Research Triangle Park, NC, USA. Electronic address: [email protected]
Type
Published Article
Journal
Reproductive toxicology (Elmsford, N.Y.)
Publication Date
Dec 01, 2019
Volume
90
Pages
102–108
Identifiers
DOI: 10.1016/j.reprotox.2019.07.013
PMID: 31415808
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Several primary sources of publicly available, quantitative dose-response data from traditional toxicology study designs relevant to predictive toxicology applications are now available, including the redeveloped U.S. Environmental Protection Agency's Toxicity Reference Database (ToxRefDB v2.0), the Health Assessment Workspace Collaborative (HAWC), and the National Toxicology Program's Chemical Program's Chemical Effects in Biological Systems (CEBS). These resources provide effect level information but modeling these data to a curve may be more informative for predictive toxicology applications. Benchmark Dose Software (BMDS) has been recognized broadly and used for regulatory applications at multiple agencies. However, the current BMDS software was not amenable to modeling large datasets. Herein we describe development and use of a Python package that implements a wrapper around BMDS, a software that requires manual input in the dose-response modeling process (i.e., best-fitting model-selection, reporting, and dose-dropping). In the Python BMDS, users can select the BMDS version, customize model recommendation logic, and export summaries of the resultant BMDS output. Further, using the Python interface, a web-based application programming interface (API) has been developed for easy integration into other software systems, pipelines, or databases. Software utility was demonstrated via modeling nearly 28,000 datasets in ToxRefDB v2.0, re-creation of an existing, published large-scale analysis, and demonstration of usage in software such as CEBS and HAWC. Python BMDS enables rapid-batch processing of dose-response datasets using a modeling software with broad acceptance in the toxicology community, thereby providing an important tool for leveraging the publicly available quantitative toxicology data in a reproducible manner. Copyright © 2019 Elsevier Inc. All rights reserved.

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