GOPArcII - new features of the GeneOntology and Pathways Architecture

Daniela Bartels1, Alexander Goesmann2, Oliver Rupp, Folker Meyer
1Daniela.Bartels@Genetik.Uni-Bielefeld.DE, Center for Genome Research, Bielefeld University; 2Alexander.Goesmann@Genetik.Uni-Bielefeld.DE, Center for Genome Research, Bielefeld University

We present GOPArcII, a new version of our comprehensive, open source framework for the integration of functional classifications and metabolic pathways. GOPArcII is based on a relational database including the GeneOntology categories and mappings provided by the GO consortium, COGs (Clusters of Orthologous Groups of proteins) categories and the KEGG pathway data. GOPArc enables a user not only to view and search this data, but also to search in genome, transcriptome and proteome data from the perspective of functional categories and metabolic pathways. We have integrated the GOPArc system with our GenDB genome annotations system and our EMMA microarray database system. GOPArc provides an object oriented Perl-API which enables programmers to easily retrieve classification and metabolic data from the database. The user interface is implemented in Perl Gtk and offers an extensible interface for data integration.