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Bioinformatics Advance Access published online on January 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk045
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Published by Oxford University Press 2006
Received October 6, 2005
Revised December 20, 2005
Accepted January 5, 2006

Article

Chemical Effects in Biological Systems (CEBS) object model for toxicology data, SysTox-OM: design and application

Sandhya Xirasagar 1 *, Scott F. Gustafson 1, Cheng-Cheng Huang 1, Qinyan Pan 1, Jennifer Fostel 2, Paul Boyer 1, B. Alex Merrick 3, Kenneth B. Tomer 3, Denny D. Chan 1, Kenneth J. Yost III 1, Danielle Choi 4, Nianqing Xiao 1, Stanley Stasiewicz 3, Pierre Bushel 3, and Michael D. Waters 3

1 Science Applications International Corporation, 20201 Century Blvd., 3rd Floor, Germantown, Maryland 20874 USA
2 Lockheed Martin Information Technologies, PO Box 12233, Research Triangle Park, North Carolina 27709 USA
3 NIEHS, National Center for Toxicogenomics, PO Box 12233, Research Triangle Park, North Carolina 27709 USA
4 Research Triangle Institute, PO Box 12194 Research Triangle Park, North Carolina 27709 USA

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


  Abstract

Motivation: The CEBS data repository is being developed to promote a systems biology approach to understanding the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein-protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts, including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner.

Results: An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source Systems Toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data (SEND; http://www.cdisc.org/models/send/v2/index.html), which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium (CDISC; http://www.cdisc.org/models/sdtm/index.html), that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms is presented here.

Availability: A Universal Modeling language (UML) depiction of the entire SysTox-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 is available at http://cebs.niehs.nih.gov/cebsdownloads. Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at http://cebs.niehs.nih.gov.

Associate Editor: Charlie Hodgman
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