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.
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).
Fostel
Jennifer
J
LIMT Lockheed Martin Information Technology (LMIT), Research Triangle Park, NC 27709, USA. fostel@niehs.nih.gov
Choi
Danielle
D
Zwickl
Craig
C
Morrison
Norman
N
Rashid
Asif
A
Hasan
Atif
A
Bao
Wenjun
W
Richard
Ann
A
Tong
Weida
W
Bushel
Pierre R
PR
Brown
Roger
R
Bruno
Maribel
M
Cunningham
Michael L
ML
Dix
David
D
Eastin
William
W
Frade
Carlos
C
Garcia
Alex
A
Heinloth
Alexandra
A
Irwin
Rick
R
Madenspacher
Jennifer
J
Merrick
B Alex
BA
Papoian
Thomas
T
Paules
Richard
R
Rocca-Serra
Philippe
P
Sansone
Assunta-Susanna
AS
Stevens
James
J
Tomer
Kenneth
K
Yang
Chihae
C
Waters
Michael
M
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
D000082:Acetaminophen