Article

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

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Bioinformatics (Impact Factor: 4.62). 05/2006; 22(7):874-82. DOI: 10.1093/bioinformatics/btk045
Source: DBLP

ABSTRACT 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.

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Available from: Alex Merrick, Aug 16, 2015
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    • "The chemical effects in biological systems (CEBS) database started off by making the expression profiles for toxicants studied at the NCT, publicly available, but then extended the system to be a repository for any toxicogenomics studies (Waters et al., 2008). The hallmark of CEBS is that the data from toxicogenomics experiments are curated, stored in the context of the study design, and integrated with other omics data or ancillary toxicological data (Fostel et al., 2005; Xirasagar et al., 2006). The National Toxicology Program at the NIEHS has acquired DrugMatrix, a toxicogenomics reference database and informatics system along with its companion toxicogenomics analysis suite resource ToxFX with the goal of making these resources freely available to public and ultimately facilitated the integration of toxicogenomics into hazard characterization (Scott Auerbach, personal communication). "
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    • "SysTox-OM is a more specific application that models changes to the genome, proteome, and metabolome following introduction of a toxicant. Furthermore, it incorporates conventional toxicology information – clinical chemistry, hematology, observations and histopathology – making it possible to evaluate the changes to the phenome across multiple time points and to target specific tissues for analysis (Xirasagar et al. 2006). For example, a user could identify a single phenotype of toxicity, identify all the drugs that are known to result in it, and compare gene and protein expression profiles in the kidney following administration of each drug to look for a common pathway, mechanism, or biomarker. "
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