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Title: Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems)

Abstract

Integration, re-use and meta-analysis of high content study data, typical of DNA microarray studies, can increase its scientific utility. Access to study data and design parameters would enhance the mining of data integrated across studies. However, without standards for which data to include in exchange, and common exchange formats, publication of high content data is time-consuming and often prohibitive. The MGED Society ( (www.mged.org)) was formed in response to the widespread publication of microarray data, and the recognition of the utility of data re-use for meta-analysis. The NIEHS has developed the Chemical Effects in Biological Systems (CEBS) database, which can manage and integrate study data and design from biological and biomedical studies. As community standards are developed for study data and metadata it will become increasingly straightforward to publish high content data in CEBS, where they will be available for meta-analysis. Different exchange formats for study data are being developed: Standard for Exchange of Nonclinical Data (SEND; (www.cdisc.org)); Tox-ML ( (www.Leadscope.com)) and Simple Investigation Formatted Text (SIFT) from the NIEHS. Data integration can be done at the level of conclusions about responsive genes and phenotypes, and this workflow is supported by CEBS. CEBS also integrates raw and preprocessed data withinmore » a given platform. The utility and a method for integrating data within and across DNA microarray studies is shown in an example analysis using DrugMatrix data deposited in CEBS by Iconix Pharmaceuticals.« less

Authors:
 [1]
  1. Global Health Sector, SRA International, Inc., LLC, Durham, North Carolina (United States), E-mail: Fostel@niehs.nih.gov
Publication Date:
OSTI Identifier:
21180468
Resource Type:
Journal Article
Journal Name:
Toxicology and Applied Pharmacology
Additional Journal Information:
Journal Volume: 233; Journal Issue: 1; Conference: 2007 TRAC: 2007 toxicology and risk assessment conference: Emerging issues and challenges in risk assessment, West Chester, OH (United States), 23-26 Apr 2007; Other Information: DOI: 10.1016/j.taap.2008.06.015; PII: S0041-008X(08)00275-5; Copyright (c) 2008 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0041-008X
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; CARBON TETRACHLORIDE; DESIGN; DNA; DRUGS; ETHANOL; GENES; ISOTHIOCYANATES; MINING; PHENOTYPE; SODIUM

Citation Formats

Fostel, Jennifer M. Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems). United States: N. p., 2008. Web. doi:10.1016/j.taap.2008.06.015.
Fostel, Jennifer M. Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems). United States. https://doi.org/10.1016/j.taap.2008.06.015
Fostel, Jennifer M. 2008. "Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems)". United States. https://doi.org/10.1016/j.taap.2008.06.015.
@article{osti_21180468,
title = {Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems)},
author = {Fostel, Jennifer M.},
abstractNote = {Integration, re-use and meta-analysis of high content study data, typical of DNA microarray studies, can increase its scientific utility. Access to study data and design parameters would enhance the mining of data integrated across studies. However, without standards for which data to include in exchange, and common exchange formats, publication of high content data is time-consuming and often prohibitive. The MGED Society ( (www.mged.org)) was formed in response to the widespread publication of microarray data, and the recognition of the utility of data re-use for meta-analysis. The NIEHS has developed the Chemical Effects in Biological Systems (CEBS) database, which can manage and integrate study data and design from biological and biomedical studies. As community standards are developed for study data and metadata it will become increasingly straightforward to publish high content data in CEBS, where they will be available for meta-analysis. Different exchange formats for study data are being developed: Standard for Exchange of Nonclinical Data (SEND; (www.cdisc.org)); Tox-ML ( (www.Leadscope.com)) and Simple Investigation Formatted Text (SIFT) from the NIEHS. Data integration can be done at the level of conclusions about responsive genes and phenotypes, and this workflow is supported by CEBS. CEBS also integrates raw and preprocessed data within a given platform. The utility and a method for integrating data within and across DNA microarray studies is shown in an example analysis using DrugMatrix data deposited in CEBS by Iconix Pharmaceuticals.},
doi = {10.1016/j.taap.2008.06.015},
url = {https://www.osti.gov/biblio/21180468}, journal = {Toxicology and Applied Pharmacology},
issn = {0041-008X},
number = 1,
volume = 233,
place = {United States},
year = {Sat Nov 15 00:00:00 EST 2008},
month = {Sat Nov 15 00:00:00 EST 2008}
}