Abstract
The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance.
Highlights
High-throughput production of biological data is becoming easier and less expensive
Given our initial interest in DNA sequencing, especially for production of expressed sequence tags (ESTs), and subsequently in microarray applications, the software package that we developed focuses on issues related to gene discovery and gene expression
Interfaces for updating tables, performing queries and visualizing the results of those queries are all either Java Server Pages (JSP) or Java GUIs deployed through Java Web Start
Summary
High-throughput production of biological data is becoming easier and less expensive. Software package that we developed focuses on issues related to gene discovery and gene expression. The core of this package is a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database, implemented in Oracle 9i. The system is: object-orientated, to facilitate adding modules; generic, so that it will perform well in a wide variety of environments; and scalable. It offers a high degree of security, to facilitate mingling of public with private data and to ensure that access to data is available only to those given permission to view it. We summarize here the fundamental characteristics of the MAGIC Database and its associated interfaces
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