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The Genopolis Microarray Database.

Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P

Department Informatics, Systemistics and Communication, University of Milano-Bicocca, Via degli Arcimboldi 8, Milano, Italy. andrea.splendiani@unimib.it.

ABSTRACT : BACKGROUND : Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood.Public repositories as well as microarray database systems that can be implemented by single laboratories exist. However, there is not yet a tool that can easily support a collaborative environment where different users with different rights of access to data can interact to define a common highly coherent content. The scope of the Genopolis database is to provide a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions. RESULTS : The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip(R) platform. It supports dynamical definition of controlled vocabularies and provides automated and supervised steps to control the coherence of data and annotations. It allows a precise control of the visibility of the database content to different sub groups in the community and facilitates exports of its content to public repositories. It provides an interactive users interface for data analysis: this allows users to visualize data matrices based on functional lists and sample characterization, and to navigate to other data matrices defined by similarity of expression values as well as functional characterizations of genes involved. A collaborative environment is also provided for the definition and sharing of functional annotation by users. CONCLUSION : The Genopolis Database supports a community in building a common coherent knowledge base and analyse it. This fills a gap between a local database and a public repository, where the development of a common coherent annotation is important. In its current implementation, it provides a uniform coherently annotated dataset on dendritic cells and macrophage differentiation.

Published 13 April 2007 in BMC Bioinformatics, 8: S21.
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