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Bioinformatics Advance Access published online on March 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth189
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 24, 2003
Revised January 14, 2004
Accepted February 25, 2004

Article

CEBS object model for systems biology data, SysBio-OM

Sandhya Xirasagar 1*, Scott Gustafson 1, B. Alex Merrick 2, Kenneth B. Tomer 2, Stanley Stasiewicz 2, Denny D. Chan 1, Kenneth J. Yost III1, John R. Yates III3, Susan Sumner 4, Nianqing Xiao 1, Michael D. Waters 2

1 Science Applications International Corporation, 20201 Century Blvd., 3rd Floor, Germantown, Maryland 20874 USA
2 NIEHS, National Center for Toxicogenomics, PO Box 12233, Research Triangle Park, North Carolina 27709 USA
3 The Scripps Research Institute, Dept of Cell Biology, 10550 North Torrey Pine Road, La Jolla, California 92037 USA
4 Paradigm Genetics, Inc., 108 TW Alexander Drive, PO Box 14528, Research Triangle Park, North Carolina 27709 USA

* To whom correspondence should be addressed. E-mail: xirasagars{at}saic.com.


  Abstract

Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledgebase 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).

Results: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, SysBio-OM. The model is comprehensive and leverages other open source efforts, namely the MAGE-OM (MicroArray Gene Expression Object Model) and the PEDRo (Proteomics Experiment Data Repository) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction data, 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.

Availability: A Universal Modeling language (UML) depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and 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.


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