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      • Department of Molecular Biology and Genetics
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      PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways

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      Author(s)
      Demir, Emek
      Babur, Özgün
      Doğrusöz, Uğur
      Gürsoy, Atilla
      Nişancı, Gürkan
      Çetin Atalay, Rengül
      Öztürk, Mehmet
      Date
      2002-06
      Source Title
      Bioinformatics
      Print ISSN
      1367-4803
      Electronic ISSN
      1367-4811
      Publisher
      Oxford University Press
      Volume
      18
      Issue
      7
      Pages
      996 - 1003
      Language
      English
      Type
      Article
      Item Usage Stats
      306
      views
      201
      downloads
      Abstract
      Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards 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. Results: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of 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, microarray generated large-scale data interpretation, disease gene identification, and drug development.
      Keywords
      Automation
      Cell function
      Computer graphics
      Computer interface
      Computer program
      Controlled study
      Data analysis
      DNA microarray
      Factual database
      Gene function
      Gene identification
      Gene sequence
      Genome
      Information processing
      Information retrieval
      Molecular Biology
      Priority journal
      Proteomics
      Cell Physiology
      Database Management Systems
      Databases
      Information storage and retrieval
      Internet
      Software design
      User-computer interface
      Permalink
      http://hdl.handle.net/11693/24660
      Published Version (Please cite this version)
      https://doi.org/10.1093/bioinformatics/18.7.996
      Collections
      • Bilkent Center for Bioinformatics (BCBI) 19
      • Department of Computer Engineering 1510
      • Department of Molecular Biology and Genetics 512
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