Science Inventory

A DATABASE FOR TRACKING TOXICOGENOMIC SAMPLES AND PROCEDURES WITH GENOMIC, PROTEOMIC AND METABONOMIC COMPONENTS

Citation:

Bao, W, J. Fostel, M. D. Waters, B. A. Merrick, D Ekman, M. Kostich, J E. Schmid, AND D J. Dix. A DATABASE FOR TRACKING TOXICOGENOMIC SAMPLES AND PROCEDURES WITH GENOMIC, PROTEOMIC AND METABONOMIC COMPONENTS. Presented at Society of Toxicology, New Orleans, LA, March 6-10, 2005.

Description:

A Database for Tracking Toxicogenomic Samples and Procedures with Genomic, Proteomic and Metabonomic Components
Wenjun Bao1, Jennifer Fostel2, Michael D. Waters2, B. Alex Merrick2, Drew Ekman3, Mitchell Kostich4, Judith Schmid1, David Dix1
Office of Research and Development, U.S. Environmental Protection Agency;1RTP, NC 27711; 3Athens, GA, 30605 and 4Cincinnati, OH, 45268.
2National Institute of Environmental Health Sciences, RTP, NC 27709.

Toxicogenomicsgenerates massive amounts of molecular datain parallel with traditional toxicological endpoints in various formats produced by researchers from different scientific disciplines.Conventional toxicology includes biochemical, histopathological and physiological endpoints, as well as information on treatments, tissues and experimental procedures. Themolecular data generated by ?omic technologies are the result of a complex series of experimental and analytical procedures.Thus, data storage and management is essential to toxicogenomics, and requires a more sophisticated system than lab notebooks and electronic spreadsheets. We developed a database for tracking Toxicogenomic Samples andProcedures (TSP) based on the MIAME-Tox guidelines and relational database theory. We report here the extension of TSP beyond genomics,to include proteomics and metabonomics components.TSP has a hierarchical structure, capturing information on study design, animal treatments, toxicological endpoints, tissue and biofluid specimens, sample characteristics and quality metrics, and linkage to subsequenttoxicogenomics data. The user-friendly interface enables researchersto easily add, edit, save, delete, and navigate different records.TSP is implemented in Microsoft Access software, permitting distribution to any laboratory running Microsoft Office. TSP creates standardized data annotation and entry systems supporting complete reporting and information exchange between researchers from different scientific disciplines. Finally, TSPfacilitates exporting data,including corresponding toxicological endpoints and details relevant to study design, into public databases such as CEBS, the Chemical Effects in Biological Systems Knowledgebase.This abstract does not necessarily reflect EPA policy.

Record Details:

Record Type: DOCUMENT (PRESENTATION/ABSTRACT)
Product Published Date: 03/06/2005
Record Last Revised: 12/22/2005
Record ID: 88158

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LABORATORY

REPRODUCTIVE TOXICOLOGY DIVISION

GAMETE AND EARLY EMBRYO BIOLOGY BRANCH