Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

MAGIC DB: An Oracle 9i Database That Integrates Microarray Data With DNA Sequence Information

Marie-Michèle Cordonnier-Pratt¹ , Feng Sun¹ , Chun Liang¹ , Haiming Wang¹ , Zheng Xia¹ , Robert M. Freeman² , Lee H. Pratt¹

¹  Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA

²  Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA

We describe a Modular Approach to a Genomic, Integrated and Comprehensive DataBase, MAGIC DB, which brings the power of a DNA sequence database to microarray applications. It includes numerous Java GUIs and JavaServer Pages that provide (a) an administrative interface for creating and administering user accounts and projects, (b) LIMS support for both sequencing and MIAME-compliant microarray experiments, (c) primary data processing pipelines, (d) quality control modules for monitoring progress in and performance of the wet lab, (e) analytical pipelines for creating and entering into the database derived data, and (f) web browser-delivered data mining and visualization interfaces designed for biologists. Java GUIs are delivered via Java Web Start, thereby providing efficient, user-friendly server-side support of client access to the database while simultaneously delivering powerful mining and visualization tools. Database modules contain the results of sequence attributes, EST clustering runs, contig assemblies and alignments, SNPs, SSRs, electronic annotations, and all the information required by the MIAME standards. Microarray data are delivered to collaborators via Oracle materialized views that are accessed by our Spotfire Server. Consequently, microarray annotations are always retrieved in real time from the DNA sequence part of MAGIC DB, providing the desired tight integration between these two activities. The DNA sequence mining and visualization tools can be used at http://fungen.org with sorghum, pine and horse EST projects. The entire package is currently being distributed on a limited scale and is being prepared for unrestricted distribution.
NSF Plant Genome Research program support is gratefully acknowledged.