MIMAS 3.0 is a Multiomics Information Management and Annotation System

Area of Science:

• Bioinformatics
• Genomics
• Molecular Biology

Background:

• Genome-wide analyses traditionally relied on microarrays for DNA sequence integrity, mRNA concentrations, and protein-DNA interactions.
• Emerging Ultra-High Throughput DNA Sequencing (UHTS) technologies offer unprecedented precision for studying these biological phenomena.
• Existing bioinformatics infrastructure requires expansion to effectively manage and analyze novel UHTS data.

Purpose of the Study:

• To enhance the Multiomics Information Management and Annotation System (MIMAS) to accommodate UHTS data.
• To integrate diverse omics data types, including microarray and next-generation sequencing data, into a unified management system.
• To provide researchers with a flexible and user-friendly platform for managing and analyzing complex genomic datasets.

Main Methods:

• MIMAS 3.0 was updated to manage data from various platforms, including Affymetrix GeneChips, Illumina BeadArrays, and the Illumina Genome Analyzer for UHTS.
• The system was adapted to handle data from SNP Chips, expression arrays (3'UTR and tiling), and promoter arrays.
• MIAME-compliant standardized vocabulary was implemented for data annotation, ensuring data quality and interoperability.

Main Results:

• MIMAS 3.0 now processes data from six types of GeneChips, two BeadArrays (mRNA and miRNA), and UHTS platforms.
• The system maintains flexibility and user-friendliness despite expanded capabilities.
• Researchers can export data in MAGE-TAB format for submission to repositories like ArrayExpress.

Conclusions:

• MIMAS has been significantly extended to become a Multiomics Information Management and Annotation System, supporting both microarray and UHTS data.
• The system is utilized by approximately 50 academic laboratories and genomics platforms in Switzerland and France.
• MIMAS 3.0 is freely available, promoting wider adoption and data sharing in the genomics community.