title: 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.
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).
authors.affiliation: LIMT Lockheed Martin Information Technology (LMIT), Research Triangle Park, NC 27709, USA. fostel@niehs.nih.gov
authors.forename: Jennifer
authors.initials: J
authors.lastname: Fostel
authors.forename: Danielle
authors.initials: D
authors.lastname: Choi
authors.forename: Craig
authors.initials: C
authors.lastname: Zwickl
authors.forename: Norman
authors.initials: N
authors.lastname: Morrison
authors.forename: Asif
authors.initials: A
authors.lastname: Rashid
authors.forename: Atif
authors.initials: A
authors.lastname: Hasan
authors.forename: Wenjun
authors.initials: W
authors.lastname: Bao
authors.forename: Ann
authors.initials: A
authors.lastname: Richard
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.forename: Pierre R
authors.initials: PR
authors.lastname: Bushel
authors.forename: Roger
authors.initials: R
authors.lastname: Brown
authors.forename: Maribel
authors.initials: M
authors.lastname: Bruno
authors.forename: Michael L
authors.initials: ML
authors.lastname: Cunningham
authors.forename: David
authors.initials: D
authors.lastname: Dix
authors.forename: William
authors.initials: W
authors.lastname: Eastin
authors.forename: Carlos
authors.initials: C
authors.lastname: Frade
authors.forename: Alex
authors.initials: A
authors.lastname: Garcia
authors.forename: Alexandra
authors.initials: A
authors.lastname: Heinloth
authors.forename: Rick
authors.initials: R
authors.lastname: Irwin
authors.forename: Jennifer
authors.initials: J
authors.lastname: Madenspacher
authors.forename: B Alex
authors.initials: BA
authors.lastname: Merrick
authors.forename: Thomas
authors.initials: T
authors.lastname: Papoian
authors.forename: Richard
authors.initials: R
authors.lastname: Paules
authors.forename: Philippe
authors.initials: P
authors.lastname: Rocca-Serra
authors.forename: Assunta-Susanna
authors.initials: AS
authors.lastname: Sansone
authors.forename: James
authors.initials: J
authors.lastname: Stevens
authors.forename: Kenneth
authors.initials: K
authors.lastname: Tomer
authors.forename: Chihae
authors.initials: C
authors.lastname: Yang
authors.forename: Michael
authors.initials: M
authors.lastname: Waters
mesh_terms: D000082:Acetaminophen / Q000633:toxicity; D000284:Administration, Oral; D000818:Animals; D035843:Biomedical Research; D003628:Database Management Systems; D016208:Databases, Factual; D004305:Dose-Response Relationship, Drug; D040901:Proteomics; D012107:Research Design; D049490:Systems Biology / Q000379:methods*; D009626:Terminology as Topic; D018675:Toxicity Tests; D043922:Toxicogenetics
chemical_list: D000082:Acetaminophen