BIOINFORMATICS Chemical Effects in Biological Systems (CEBS) Object Model for Toxicology Data, SysTox-OM: Design and Application

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 userfriendly 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

CEBS—Chemical Effects in Biological Systems:

doi:10.1093/nar/gkm75