Patikaweb: Patika veritabanındaki yolak verisine erişmek ve görüntülemek için ağ hizmeti

After completion of Human Genome Project, there has been an exponential in-crease in the available biological data. Although there has been an enormous ef-fort for creating ontologies, standards and tools, current bioinformatics infrastruc-ture is far from coping with this data. The Patika Project aims to provide thecommunity an integrated environment for modeling, analyzing and integratingcellular processes.Patika project develops software tools providing access, visualization andanalysis on the data in Patika database. In this thesis, we present analysis, de-sign and implementation of Patikaweb, a Web-service having a user-friendly in-terface without requiring any registrations, installations. To achieve an enhanceddata analysis , Patikaweb provides a multiple-view schema , compartments andcompound graphs for visualizing molecular complexes, pathways and black-boxreactions.Querying component supports SQL-like queries and an array of graph-theoretic queries for finding feedback loops, common targets and regulators, orinteresting subgraphs based on user?s genes of interest. Constructed models canbe saved in XML, exported to standard formats such as BioPAX, SBML or con-verted to static images. A highly interactive and user friendly querying interfaceis supported with Patikaweb.Visual representation of complex information in pathway research is very im-portant. The information should be presented with high coverage, while providinga user friendly interface. In this thesis we also present a new approach to visualizecomplex pathway information coping with the limitations introduced by ontologyand graphical representation.iiiiiPatikaweb ?s unique visualization and querying features fill an important gapin the pool of currently available tools and databases.Keywords: Bioinformatics, pathway visualization, complex view management,Web service.