CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data

Abstract

CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. CEBS is designed to permit the user to query the data using the study conditions, the subject responses and then, having identified an appropriate set of subjects, to move to the microarray module of CEBS to carry out gene signature and pathway analysis. Scope of CEBS: CEBS currently holds 22 studies of rats, four studies of mice and one study of Caenorhabditis elegans. CEBS can also accommodate data from studies of human subjects. Toxicogenomics studies currently in CEBS comprise over 4000 microarray hybridizations, and 75 2D gel images annotated with protein identification performed by MALDI and MS/MS. CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Additionally, clinical chemistry and histopathology findings from over 1500 animals are included in CEBS. CEBS/BID: The BID (Biomedical Investigation Database) is another component of the CEBS system. BID is a relational database used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee (in preparation). BID has been shared with Health Canada and the US Environmental Protection Agency. CEBS is available at http://cebs.niehs.nih.gov. BID can be accessed via the user interface from https://dir-apps.niehs.nih.gov/arc/. Requests for a copy of BID and for depositing data into CEBS or BID are available at http://www.niehs.nih.gov/cebs-df/.

Figure 1.

Architecture of CEBS. The green box represents CEBS, and shows the relationships between CEBS components: the SysBio and SysTox Object models, internal databases and file structure and the caBIO annotation engine and external annotation resources. User access is represented using blue terminals.

Figure 2.

Workflows in CEBS. The gray box represents CEBS. Search and query workflows are shown in tan, data in green and analysis and annotation in yellow. Entry points for users are shown with blue arrows, and data download points with magenta arrows.

Figure 3.

Screenshots of three novel CEBS displays, the Study list and disparate associated data types (A), the Study Timeline (Boxes with X indicates an event occurred at that time point. Details of protocols are accessible via links at left) (B) and the Study Group Grid (C).

Figure 4.

BID architecture. Each table is labeled, and contains the primary and foreign keys to allow relationships to be easily discerned. The different modules of BID are enclosed in boxes. Study data tables are enclosed in aqua, study protocols in red, microarray workflow and data are in dark blue, study stressors in spring green, study events in olive green, study subject characteristics in orange, study specimens in magenta. Study tables, including publication and access rights, are not outlined.