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 - PubMed (original) (raw)
. 2005 Dec;88(2):585-601.
doi: 10.1093/toxsci/kfi315. Epub 2005 Sep 8.
Danielle Choi, Craig Zwickl, Norman Morrison, Asif Rashid, Atif Hasan, Wenjun Bao, Ann Richard, Weida Tong, Pierre R Bushel, Roger Brown, Maribel Bruno, Michael L Cunningham, David Dix, William Eastin, Carlos Frade, Alex Garcia, Alexandra Heinloth, Rick Irwin, Jennifer Madenspacher, B Alex Merrick, Thomas Papoian, Richard Paules, Philippe Rocca-Serra, Assunta-Susanna Sansone, James Stevens, Kenneth Tomer, Chihae Yang, Michael Waters
Affiliations
- PMID: 16150882
- DOI: 10.1093/toxsci/kfi315
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 et al. Toxicol Sci. 2005 Dec.
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 (A. N. Heinloth et al., 2004, Toxicol. Sci. 80, 193-202).
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