title: Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.
abstract: 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.
authors.affiliation: Science Applications International Corporation, 20201 Century Boulevard, 3rd Floor, Germantown, MD 20874, USA. xirasagars@saic.com
authors.forename: Sandhya
authors.initials: S
authors.lastname: Xirasagar
authors.forename: Scott F
authors.initials: SF
authors.lastname: Gustafson
authors.forename: Cheng-Cheng
authors.initials: CC
authors.lastname: Huang
authors.forename: Qinyan
authors.initials: Q
authors.lastname: Pan
authors.forename: Jennifer
authors.initials: J
authors.lastname: Fostel
authors.forename: Paul
authors.initials: P
authors.lastname: Boyer
authors.forename: B Alex
authors.initials: BA
authors.lastname: Merrick
authors.forename: Kenneth B
authors.initials: KB
authors.lastname: Tomer
authors.forename: Denny D
authors.initials: DD
authors.lastname: Chan
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Yost
authors.forename: Danielle
authors.initials: D
authors.lastname: Choi
authors.forename: Nianqing
authors.initials: N
authors.lastname: Xiao
authors.forename: Stanley
authors.initials: S
authors.lastname: Stasiewicz
authors.forename: Pierre
authors.initials: P
authors.lastname: Bushel
authors.forename: Michael D
authors.initials: MD
authors.lastname: Waters
mesh_terms: 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*