Abstract
BackgroundThe high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis of mRNA concentrations. Local array data management solutions are instrumental for efficient processing of the results and for subsequent uploading of data and annotations to a global certified data repository at the EBI (ArrayExpress) or the NCBI (GeneOmnibus).DescriptionTo facilitate and accelerate annotation of high-throughput expression profiling experiments, the Microarray Information Management and Annotation System (MIMAS) was developed. The system is fully compliant with the Minimal Information About a Microarray Experiment (MIAME) convention. MIMAS provides life scientists with a highly flexible and focused GeneChip data storage and annotation platform essential for subsequent analysis and interpretation of experimental results with clustering and mining tools. The system software can be downloaded for academic use upon request.ConclusionMIMAS implements a novel concept for nation-wide GeneChip data management whereby a network of facilities is centered on one data node directly connected to the European certified public microarray data repository located at the EBI. The solution proposed may serve as a prototype approach to array data management between research institutes organized in a consortium.
Highlights
The high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis of mRNA concentrations
The classical architecture of GeneChips is based on synthesizing a set of oligonucleotide probes complementary to mRNAs encoded by putative genes previously defined during an error-prone process called genome annotation [15]
We propose a network solution for GeneChip data management whereby one location in a given consortium provides a central facility hosting the data and system and enabling scientists to describe them via the Internet according to the international Microarray Experiment (MIAME) convention
Summary
MIMAS is a MIAME-compliant relational database implemented in Oracle (and portable into MySQL) for highdensity oligonucleotide microarray data archiving, anno-. The Auxiliary Services, Plug-ins & Loaders component is a set of Perl scripts and daemons which manage various tasks such as transformation of completed microarray experiments, job requests executed by users, and integration of data with external databases. Since the software components required by MIMAS (MySQL, Oracle, Perl, Apache, mod_perl) are capable of running on many common operating systems (UNIX, Linux, Windows), the distribution can be installed on any one or a mixture of these. API (Application Programmer Interface), CPAN (Comprehensive Perl Archive Network), DBMS (Database Management System), GCOS (GeneChip Operating System), GUI (Graphical User Interface), HTTP (Hypertext Transfer Protocol), MAGE (MicroArray and Gene Expression), MAS (Microarray Analysis Suite), MGED (Microarray Gene Expression Data), MIAME (Minimal Information about a Microarray Experiment), RMA (Robust Multi-array Average), SOAP (Simple Object Access Protocol), SSL (Secure Sockets Layer).
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