CEBS Object Models
Motivation for Development
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.
SysBio Object Model
Design Approach and Results
To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model.
SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation.
Learn More
You may become more familiar with SysBio by either browsing SysBio online or downloading the Rational Rose mdl file. Both constitute UML representations of the SysBio object model.
Literature
A paper describing SysBio-OM has recently been published in Bioinformatics. A PubMed link to the publication abstract is available (a Bioinformatics subscription is required to view the full paper).
SysTox Object Model
Design Approach and Results
SysTox-OM is an open source Systems Toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM is designed to foster the efficient capture, storage, retrieval, and exchange of study design and conventional toxicology information such as clinical chemistry, hematology, clinical observations, and histopathology.
The SysTox model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data (SEND), which is a data standard for capturing toxicological information for animal studies; and Clinical Data Interchange Standards Consortium (CDISC), which serves as a standard for the exchange of clinical data.
Learn More
You may become more familiar with SysTox by either browsing SysTox online or downloading the Rational Rose mdl file. Both constitute UML representations of the SysTox object model.
Literature
A paper describing SysTox-OM has recently been submitted.
