Abstract
ebTrack is being developed as an integrated bioinformatics system for environmental research and analysis by addressing the issues of integration, curation, management, first level analysis and interpretation of environmental and toxicological data from diverse sources. It is based on enhancements to the US FDA developed ArrayTrack system through additional analysis modules for gene expression data as well as through incorporation and linkages to modules for analysis of proteomic and metabonomic datasets that include tandem mass spectra. ebTrack uses a client-server architecture with the free and open source PostgreSQL as its database engine, and java tools for user interface, analysis, visualization, and web-based deployment. Several predictive tools that are critical for environmental health research are currently supported in ebTrack, including Significance Analysis of Microarray (SAM). Furthermore, new tools are under continuous integration, and interfaces to environmental health risk analysis tools are being developed in order to make ebTrack widely usable. These health risk analysis tools include the Modeling ENvironment for TOtal Risk studies (MENTOR) for source-to-dose exposure modeling and the DOse Response Information ANalysis system (DORIAN) for health outcome modeling. The design of ebTrack is presented in detail and steps involved in its application are summarized through an illustrative application.
Highlights
Toxicogenomics [1,2], with its emphasis on analysis of gene expression, metabolic pathways, and regulatory networks, has revolutionized the field of toxicology.Toxicogenomics combines the technologies of genomics, proteomics, and metabonomics to identify and characterize mechanisms of action of known and suspected toxicants as well as toBMC Proceedings 2009, 3(Suppl 2):S5 http://www.biomedcentral.com/1753-6561/3/S2/S5 determine predictive biomarkers for supporting health risk assessments
Such a system must implement the following three critical features in order to facilitate the successful analysis and interpretation of toxicogenomics studies: (1) Centralized data management and annotation of data from various types of "omics" experiments and multiple steps within each experiment. This facilitates a common starting point for comparative application of independent tools and analysis methods by different researchers; and analysis of data from DNA microarray experiments for humans, mouse and rat; and (c) it is not a public repository and, still requires significant scale up in order to accommodate data from diverse laboratories involved in environmental health research; and (d) it was originally developed by the US FDA for regulatory purposes, and incorporates a set of well-established tools that comprise only a small subset of the tools required to address the broad scope and variation in data sets encountered in environmental health research
Multiple factors necessitate the development of a new system based on ArrayTrackTM: (a) it is based on a client-server architecture involving expensive database software (Oracle; http:/ /www.oracle.com); (b) it is limited to the management
Summary
Toxicogenomics [1,2], with its emphasis on analysis of gene expression, metabolic pathways, and regulatory networks, has revolutionized the field of toxicology. An integrated bioinformatics system that enables consistent analysis of collective "omics" data sets and meta data is crucial for toxicogenomics research Such a system must implement the following three critical features in order to facilitate the successful analysis and interpretation of toxicogenomics studies:. (2) Provision for rapid data analysis via an intuitive user interface This facilitates easy application of standard tools for quickly searching, filtering, applying mathematical and statistical operations, and graphically visualizing various "omics" data sets; and (3) Provision for informed data interpretation through interfaces to relevant knowledge bases of gene annotation, protein function and pathways. The main objective in the development of ebTrack is to provide a one-stop solution for environmental research by addressing the issues of integration, curation, management, analysis and interpretation of environmental and toxicological data from diverse types of experiments encountered in environmental health research
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