Integration of data in pathogenomics is achieved here considering three different levels of cellular complexity: (i) genome and comparative genomics, (ii) enzyme cascades and pathway analysis, (iii) networks including metabolic network analysis. After direct sequence annotation exploiting tools for protein domain annotation (e.g. AnDOM) and analysis of regulatory elements (e.g. the RNA analyzer tool) the analysis results from extensive comparative genomics are integrated for the first level, pathway alignment adds data for the pathway level, elementary mode analysis and metabolite databanks add to the third level of cellular complexity. For efficient data integration of all data the XML based platform myBSMLStudio2003 is discussed and developed here. It integrates XQuery capabilities, automatic scripting updates for sequence annotation and a JESS expert system shell for functional annotation. In the context of genome annotation platforms in place (GenDB, PEDANT) these different tools and approaches presented here allow improved functional genome annotation as well as data integration in pathogenomics.
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