ToxSci Advance Access originally published online on September 8, 2005
Toxicological Sciences 2005 88(2):585-601; doi:10.1093/toxsci/kfi315
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Published by Oxford University Press 2005.
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
* LIMT Lockheed Martin Information Technology (LMIT), Research Triangle Park, North Carolina 27709; Lilly Research Laboratory, Greenfield, Indiana 46140; National Environmental Research Council (NERC), University of Manchester, Manchester M13 9PL, U.K.; Alpha-Gamma Technologies, Inc., Raleigh, North Carolina 27609; ¶ U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; || U.S. National Center for Toxicogenomics Research (NCTR), Jefferson, Arkansas 72079; ||| U.S. National Center for Toxicogenomics (NCT), Research Triangle Park, North Carolina 27709; |||| Glaxo-SmithKline, Inc., Research Triangle Park, North Carolina 27709; # U.S. National Toxicology Program, Research Triangle Park, North Carolina 27709; ** Xybion, Inc., Cedar Knolls, New Jersey; The European Bioinformatics Institute (EMBL-EBI) Hinxton, Wellcome Trust Genome Campus, Cambridge CB10, U.K.; U.S. Food and Drug Administration (FDA) Center for Drug Evaluation and Research, Rockville, Maryland 20857; and Leadscope, Inc., Columbus, Ohio 43215
Received July 19, 2005; accepted September 2, 2005
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 (A. N. Heinloth et al., 2004, Toxicol. Sci. 80, 193–202).
Key Words: Chemical Effects in Biological Systems (CEBS) Knowledgebase; toxicogenomics study protocols; toxicity endpoint data; acetaminophen; phenotypic anchor.
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