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      • Dept. of Molecular Biology and Genetics - Master's degree
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      •   BUIR Home
      • University Library
      • Bilkent Theses
      • Theses - Department of Molecular Biology and Genetics
      • Dept. of Molecular Biology and Genetics - Master's degree
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      Modeling cellular processes with PATİKA

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      Author(s)
      Demir, Emek
      Advisor
      Çetin-Atalay, Rengül
      Date
      2001
      Publisher
      Bilkent University
      Language
      English
      Type
      Thesis
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      Abstract
      Availability of the sequences of entire genomes shifts the scientific curiosity toward the identification of function of the genomes in large scale as in genome studies. In the near future data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. We define an ontology for a comprehensive representation of cellular events. The model presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporations of the stored data, as well as multiple levels of abstraction. Based on this model, we present an integrated environment named PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition). PATIKA is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that PATIKA will be a valuable tool for rapid knowledge acquisition; micro array generated large-scale data interpretation; disease gene identification and drug development
      Keywords
      bioinformatics
      ontology
      automated layout
      object oriented database
      cellular pathways
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      http://hdl.handle.net/11693/14564
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      • Dept. of Molecular Biology and Genetics - Master's degree 167
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