Open AccessMAGIC Database and interfaces: an integrated package for gene discovery and expression
Author(s) -
CordonnierPratt MarieMichèle,
Liang Chun,
Wang Haiming,
Kolychev Dmitri S.,
Sun Feng,
Freeman Robert,
Sullivan Robert,
Pratt Lee H.
Publication year - 2004
Publication title -
comparative and functional genomics
Language(s) - English
Resource type - Journals
eISSN - 1532-6268
pISSN - 1531-6912
DOI - 10.1002/cfg.399
Subject(s) - magic (telescope) , relational database , computer science , annotation , database , cluster analysis , the internet , information retrieval , world wide web , artificial intelligence , physics , quantum mechanics
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 M odular A pproach to a G enomic, I ntegrated and C omprehensive (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. Copyright © 2004 John Wiley & Sons, Ltd.