MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.
BACKGROUND
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. 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).


METHODS
To 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.


CONCLUSIONS
MIMAS 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.
Hermida
Leandro
L
Biozentrum and Swiss Institute of Bioinformatics Klingelbergstrasse 50-70 CH-4056 Basel Switzerland. leandro.hermida@unibas.ch
Schaad
Olivier
O
Demougin
Philippe
P
Descombes
Patrick
P
Primig
Michael
M
D003628:Database Management Systems; D030541:Databases, Genetic; D004282:Documentation / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology; D012984:Software; D014584:User-Computer Interface