Xirasagar Sandhya, Gustafson Scott, Merrick B Alex, Tomer Kenneth B, Stasiewicz Stanley, Chan Denny D, Yost Kenneth J, Yates John R, Sumner Susan, Xiao Nianqing, Waters Michael D
Science Applications International Corporation, 20201 Century Building, 3rd Floor, Germantown, MD 20874, USA.
Bioinformatics. 2004 Sep 1;20(13):2004-15. doi: 10.1093/bioinformatics/bth189. Epub 2004 Mar 25.
To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics).
To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here.
A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.
为推动采用系统生物学方法来理解环境应激源的生物学效应，正在开发生物系统中的化学效应（CEBS）知识库，以便以系统友好的方式存储来自多个复杂数据流的数据，从而满足用户的广泛查询需求。通过单一对象模型实现统一的数据表示将极大地有助于集成数据存储和管理，并促进软件的重用，以分析和显示来自各种差异表达或差异谱技术的数据。数据流包括但不限于基因表达分析（转录组学）、蛋白质表达和蛋白质 - 蛋白质相互作用分析（蛋白质组学）以及低分子量代谢物水平的变化（代谢组学）。
为了在CEBS系统中整合微阵列基因表达、蛋白质组学和代谢组学数据，我们设计了一个对象模型，即系统生物学对象模型（SysBio - OM）。该模型全面且借鉴了其他开源成果，即微阵列基因表达对象模型（MAGE - OM）和蛋白质组学实验数据存储库（PEDRo）对象模型。SysBio - OM通过扩展MAGE - OM来设计，以表示蛋白质表达数据元素（包括来自PEDRo的那些）、蛋白质 - 蛋白质相互作用和代谢组学数据。SysBio - OM通过促进捕获实验所需的最少注释来推动数据表示和数据质量的标准化。这种标准化提高了数据挖掘和解释的准确性。本文展示了可在各种计算平台上实现的开源SysBio - OM模型。
整个SysBio - OM的通用建模语言描述可在http://cebs.niehs.nih.gov/SysBioOM/获取。Rational Rose对象模型包根据开源许可进行分发，允许无限制的学术和商业使用，可在http://cebs.niehs.nih.gov/cebsdownloads获取。正在构建数据库和接口以实现该模型，并将在http://cebs.niehs.nih.gov供公众使用。
