CEBS object model for systems biology data, SysBio-OM

摘要: Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, Chemical Effects in Biological Systems (CEBS) knowledge base is being developed house data from multiple complex streams friendly manner that will accommodate extensive querying users. Unified representation via single object model greatly aid integrating storage and management, facilitate reuse software analyze display resulting diverse differential expression or profile technologies. Data include, but are not limited to, gene analysis (transcriptomics), protein protein--protein interaction (proteomics) changes low molecular weight metabolite levels (metabolomics). Results: enable integration microarray expression, proteomics metabolomics CEBS system, we designed an model, Biology Object Model (SysBio-OM). The comprehensive leverages other open source efforts, namely MicroArray Gene Expression (MAGE-OM) Proteomics Experiment Repository (PEDRo) model. SysBio-OM by extending MAGE-OM represent elements (including those PEDRo), data. promotes standardization quality facilitating capture minimum annotation required for experiment. Such refines accuracy mining interpretation. which can be implemented on varied computing platforms presented here. Availability: A universal modeling language depiction entire available at http://cebs.niehs.nih.gov/SysBioOM/. Rational Rose package distributed under license permits unrestricted academic commercial use http://cebs.niehs.nih.gov/cebsdownloads. database interface built implement public http://cebs.niehs.nih.gov.