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Database of Pharmacokinetic Time-Series Data and Parameters for Evaluating the Safety of Environmental Chemicals
Citation:
Sayre, R., J. Wambaugh, AND C. Grulke. Database of Pharmacokinetic Time-Series Data and Parameters for Evaluating the Safety of Environmental Chemicals. Presented at American Chemical Society Spring Meeting, Orlando, FL, March 31 - April 04, 2019. https://doi.org/10.23645/epacomptox.8023229
Impact/Purpose:
Abstract and poster for presentation at the American Chemical Society Spring Meeting in April 2019. An understanding of pharmacokinetics can be developed using in vitro assays and in silico models, but the quantitative uncertainty cannot be determined without in vivo data for external validation. To address this need, we present workflow for extraction of pharmacokinetic time series data from publication and the resulting public database of time-series from almost 600 studies in humans or test animals.
Description:
Time courses of compound concentrations in plasma are used to evaluate the relationship between external administered doses and internal tissue exposures. This type of experimental data is rarely available for the thousands of chemicals to which people may potentially be exposed. An understanding of pharmacokinetics can be developed using in vitro assays and in silico models, but the quantitative uncertainty cannot be determined without in vivo data for external validation. To address this need, we present workflow for extraction of pharmacokinetic time series data from publication and the resulting public database of time-series from almost 600 studies in humans or test animals. This database currently contains over 150 environmentally-relevant chemicals and their metabolites by all major administration routes with concentrations measured in blood/plasma, tissues, and/or excreta. All information in the database was sourced from either open databases or published literature identified using a suite of classifiers from SciKitLearn trained on the term frequency-inverse document frequency (TD-IDF) of the documents’ abstracts. Both the identified sources and the extracted pharmacokinetic time-series are stored in a MySQL database with detailed, manually curated metadata. Concentration-time points were manually captured using the webtool WebPlotDigitizer. Data in all fields are normalized to facilitate comparisons, but original values are retained for transparency. Plots of the data are intended for dissemination through the US EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), along with this associated optimized pharmacokinetic summary parameters (e.g. area under the curve, volume of distribution) calculated using the R package invivopkfit. To facilitate data sharing we can accommodate and encourage submissions of structured published data on any compound. This abstract does not necessarily reflect U.S. EPA policy.
URLs/Downloads:
DOI: Database of Pharmacokinetic Time-Series Data and Parameters for Evaluating the Safety of Environmental Chemicals
SAYRE_ACS_CVT_ACS_POSTER_20190322.PDF (PDF, NA pp, 1104.939 KB, about PDF)