Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.
BACKGROUND
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.


BACKGROUND
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


BACKGROUND
xirasagars@saic.com


BACKGROUND
Supplementary data are available at Bioinformatics online.
Xirasagar
Sandhya
S
Science Applications International Corporation, 20201 Century Boulevard, 3rd Floor, Germantown, MD 20874, USA. xirasagars@saic.com
Gustafson
Scott F
SF
Huang
Cheng-Cheng
CC
Pan
Qinyan
Q
Fostel
Jennifer
J
Boyer
Paul
P
Merrick
B Alex
BA
Tomer
Kenneth B
KB
Chan
Denny D
DD
Yost
Kenneth J
KJ
Choi
Danielle
D
Xiao
Nianqing
N
Stasiewicz
Stanley
S
Bushel
Pierre
P
Waters
Michael D
MD
D019295:Computational Biology; D003628:Database Management Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D011381:Programming Languages; D040901:Proteomics; D012985:Software Design; D043922:Toxicogenetics / Q000379:methods*