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Bioinformatics Advance Access published online on January 22, 2004
Bioinformatics, doi:10.1093/bioinformatics/btg428
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 19, 2003
Revised August 9, 2003
Accepted August 11, 2003

Article

RAD and the RAD Study-Annotator: an approach to collection, organization, and exchange of all relevant information for high-throughput gene expression studies

E. Manduchi 1*, G. R. Grant 1, H. He 1, J. Liu 1, M. D. Mailman 1, A. D. Pizarro 1, P. L. Whetzel 1, C. J. Stoeckert Jr.1

1 Center for Bioinformatics, University of Pennsylvania, 14th floor Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104-6021, USA

* To whom correspondence should be addressed. E-mail: manduchi{at}pcbi.upenn.edu.


  Abstract

Motivation: Gene expression array technology has become increasingly widespread among researchers who recognize its numerous promises. At the same time, bench biologists and bioinformaticians have come to increasingly appreciate the importance of establishing a collaborative dialog from the onset of a study and of collecting and exchanging detailed information on the many experimental and computational procedures using a structured mechanism. This is crucial for adequate analyses of this kind of data.

Results: The RNA Abundance Database (RAD: http://www.cbil.upenn.edu/RAD) provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). RAD is part of a more general Genomics Unified Schema (GUS: http://www.gusdb.org), which includes a richly annotated gene index (http://www.allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems.

Availability: The system is freely available. Information on how to obtain it and how to install it can be found at http://www.cbil.upenn.edu/RAD/RAD-installation.htm.


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