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ToxSci Advance Access published online on September 8, 2005
Toxicological Sciences, doi:10.1093/toxsci/kfi315
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Published by Oxford University Press 2005.
Received July 19, 2005
Accepted September 2, 2005

Systems Toxicology

Chemical Effects in Biological Systems - Data Dictionary (CEBS-DD): A Compendium of Terms for the Capture and Integration of Biological Study Design Description, Conventional Phenotypes and 'Omics Data

Jennifer Fostel 1*, Danielle Choi 1, Craig Zwickl 2, Norman Morrison 3, Asif Rashid 4, Atif Hasan 5, Wenjun Bao 6, Ann Richard 6, Weida Tong 7, Pierre R. Bushel 8, Roger Brown 9, Maribel Bruno 8, Michael L. Cunningham 10, David Dix 6, William Eastin 10, Carlos Frade 11, Alex Garcia 12, Alexandra Heinloth 8, Rick Irwin 10, Jennifer Madenspacher 8, B. Alex Merrick 8, Thomas Papoian 13, Richard Paules 8, Philippe Rocca-Serra 12, Assunta-Susanna Sansone 12, James Stevens 2, Kenneth Tomer 8, Chihae Yang 14, and Michael Waters 8

1 LIMT Lockheed Martin Information Technology (LMIT), Research Triangle Park, NC, 27709
2 Lilly Research Laboratory, Greenfield, IN, 46140
3 National Environmental Research Council (NERC), University of Manchester, Manchester M13 9PL, UK
4 LIMT Lockheed Martin Information Technology (LMIT), Research Triangle Park, NC, 27709; Alpha-Gamma Technologies, Inc., Raleigh NC 27609
5 Alpha-Gamma Technologies, Inc., Raleigh NC 27609
6 U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
7 U.S. National Center for Toxicogenomics Research (NCTR), Jefferson, AR 72079
8 U.S. National Center for Toxicogenomics (NCT), Research Triangle Park, NC, 27709
9 Glaxo-SmithKline, Inc. Research Triangle Park, NC, 27709
10 U.S. National Toxicology Program, Research Triangle Park, NC, 27709
11 Xybion, Inc., Cedar Knolls, NJ
12 The European Bioinformatics Institute (EMBL-EBI) Hinxton, Wellcome Trust Genome Campus, Cambridge CB10, UK
13 U.S. Food and Drug Administration (FDA) Center for Drug Evaluation and Research, Rockville, MD 20857
14 Leadscope, Inc., Columbus OH, 43215

* To whom correspondence should be addressed.
Jennifer Fostel, E-mail: fostel{at}niehs.nih.gov


  Abstract

A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical pathology and histopathology). A Study is generally an experiment carried out during a period of time for the purpose of obtaining data, and the Study Design Description captures the methods, timing and organization of the Study. The CEBS Data Dictionary (CEBS-DD) has been designed to define and organize terms in an attempt to standardize nomenclature needed to describe a toxicogenomics Study in a structured yet intuitive format and provide a flexible means to describe a Study as conceptualized by the investigator. The CEBS-DD will organize and annotate information from a variety of sources, thereby facilitating the capture and display of toxicogenomics data in biological context in CEBS, i.e. associating molecular events detected in highly-parallel data with the toxicology / pathology phenotype as observed in the individual Study Subjects and linked to the experimental treatments. The CEBS-DD has been developed with a focus on acute toxicity studies, but with a design that will permit it to be extended to other areas of toxicology and biology with the addition of domain-specific terms. To illustrate the utility of the CEBS-DD, we present an example of integrating data from two proteomics and transcriptomics studies of the response to acute acetaminophen toxicity.


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