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EGOMiner, stands for enhanced gene ontology mining system, is a CORBA based tool developed for genomic and proteomic data analysis. One key function of EGOMiner is to provide biological data interpretation based on gene ontology with quantitative and statistical analysis and visualization by direct acyclic graph. Cross comparison of multiple experimental studies is supported. The other function is quality analysis of microarray chip images. The input is raw chip data and output is visualization of the data quality of the chip image. This is system significantly improves the GoMiner system that was designed and developed by the authors.