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Bioinformatics Advance Access originally published online on January 12, 2006
Bioinformatics 2006 22(7):874-882; doi:10.1093/bioinformatics/btk045
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Published by Oxford University Press 2006
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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 3, Paul Boyer 1, B. Alex Merrick 2, Kenneth B. Tomer 2, Denny D. Chan 1, Kenneth J. Yost, III 1, Danielle Choi 4, Nianqing Xiao 1, Stanley Stasiewicz 2, Pierre Bushel 2 and Michael D. Waters 2

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

*To whom correspondence should be addressed.

Motivation: The CEBS data repository is being developed to promote a systems biology approach to understand 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 (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 (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 and 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

Contact: xirasagars{at}saic.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on October 6, 2005; revised on December 20, 2005; accepted on January 5, 2006

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