当前位置： SCI文献检索 > ENVIRONMENTAL HEALTH PERSPECTIVES期刊下所有文献 > Database development in toxicogenomics: issues and efforts.

Database development in toxicogenomics: issues and efforts.

Abstract：

:The marriage of toxicology and genomics has created not only opportunities but also novel informatics challenges. As with the larger field of gene expression analysis, toxicogenomics faces the problems of probe annotation and data comparison across different array platforms. Toxicogenomics studies are generally built on standard toxicology studies generating biological end point data, and as such, one goal of toxicogenomics is to detect relationships between changes in gene expression and in those biological parameters. These challenges are best addressed through data collection into a well-designed toxicogenomics database. A successful publicly accessible toxicogenomics database will serve as a repository for data sharing and as a resource for analysis, data mining, and discussion. It will offer a vehicle for harmonizing nomenclature and analytical approaches and serve as a reference for regulatory organizations to evaluate toxicogenomics data submitted as part of registrations. Such a database would capture the experimental context of in vivo studies with great fidelity such that the dynamics of the dose response could be probed statistically with confidence. This review presents the collaborative efforts between the European Molecular Biology Laboratory-European Bioinformatics Institute ArrayExpress, the International Life Sciences Institute Health and Environmental Science Institute, and the National Institute of Environmental Health Sciences National Center for Toxigenomics Chemical Effects in Biological Systems knowledge base. The goal of this collaboration is to establish public infrastructure on an international scale and examine other developments aimed at establishing toxicogenomics databases. In this review we discuss several issues common to such databases: the requirement for identifying minimal descriptors to represent the experiment, the demand for standardizing data storage and exchange formats, the challenge of creating standardized nomenclature and ontologies to describe biological data, the technical problems involved in data upload, the necessity of defining parameters that assess and record data quality, and the development of standardized analytical approaches.

journal_name

Environ Health Perspect

journal_title

Environmental health perspectives

authors

Mattes WB,Pettit SD,Sansone SA,Bushel PR,Waters MD

doi

10.1289/ehp.6697

subject

Has Abstract

pub_date

2004-03-01 00:00:00

pages

495-505

issue

eissn

0091-6765

issn

1552-9924

journal_volume

112

pub_type

杂志文章,评审

在线工具

Database development in toxicogenomics: issues and efforts.