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      An ontology for collaborative construction and analysis of cellular pathways

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      Author(s)
      Demir, Emek
      Babur, Özgün
      Doğrusöz, Uğur
      Gürsoy, Atilla
      Ayaz, Aslı
      Güleşır, Gürcan
      Nişancı, Gürkan
      Çetin Atalay, Rengül
      Date
      2004-02-12
      Source Title
      Bioinformatics
      Print ISSN
      1367-4803
      Electronic ISSN
      1367-4811
      Publisher
      Oxford University Press
      Volume
      20
      Issue
      3
      Pages
      349 - 356
      Language
      English
      Type
      Article
      Item Usage Stats
      263
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      202
      downloads
      Abstract
      Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated. Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology. © Oxford University Press 2004; All rights reserved.
      Keywords
      Cell activity
      Computer program
      Controlled study
      Factual
      Gene function
      Gene identification
      Genome analysis
      Mathematical computing
      Molecular interaction
      Molecular mechanics
      Priority journal
      Validation process
      Biopolymers
      Cell Physiology
      Database management systems
      Databases
      Information storage and retrieval
      Models
      Signal transduction
      Software
      Systems Iitegration
      User-computer interface
      Biological
      Permalink
      http://hdl.handle.net/11693/24320
      Published Version (Please cite this version)
      http://dx.doi.org/10.1093/bioinformatics/btg416
      Collections
      • Bilkent Center for Bioinformatics (BCBI) 19
      • Department of Computer Engineering 1510
      • Department of Molecular Biology and Genetics 512
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