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
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
复制标题
DOI：
10.1093/toxsci/kfi315
复制
发表时间：
2005-12-01
影响因子：
3.8
通讯作者：
Waters, M
中科院分区：
文献类型：
--
作者：
Fostel, J;Choi, D;Waters, M
设计生物系统化学效应(CEBS)知识库的一个关键组成部分是获取毒素基因组学研究方案和毒性终点数据(临床病理学和组织病理学)的策略。研究通常是为了获得数据而在一段时间内进行的实验，研究设计说明记录了研究的方法、时间和组织。CEBS数据词典(CEBS-DD)旨在定义和组织术语，试图以结构化但直观的格式标准化描述毒性基因组学研究所需的命名法，并提供一种灵活的手段来描述研究人员概念化的研究。CEBS-DD将组织和注释来自各种来源的信息，从而促进在CEBS的生物学背景下捕获和显示毒素基因组数据，即将在高度平行的数据中检测到的分子事件与在个别研究对象中观察到的毒理学/病理表型联系起来，并与实验处理相联系。CEBS-DD的开发侧重于急性毒性研究，但其设计将允许通过添加特定领域的术语将其扩展到毒理学和生物学的其他领域。为了说明CEBS-DD的实用性，我们提供了一个整合来自急性对乙酰氨基酚中毒反应的两个蛋白质组学和转录组学研究的数据的例子(A.N.Heinloth等人，2004年，Toxicol。SCI。80、193-202)。
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).