PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways

dc.citation.epage1003en_US
dc.citation.issueNumber7en_US
dc.citation.spage996en_US
dc.citation.volumeNumber18en_US
dc.contributor.authorDemir, Emeken_US
dc.contributor.authorBabur, Özgünen_US
dc.contributor.authorDoğrusöz, Uğuren_US
dc.contributor.authorGürsoy, Atillaen_US
dc.contributor.authorNişancı, Gürkanen_US
dc.contributor.authorÇetin Atalay, Rengülen_US
dc.contributor.authorÖztürk, Mehmeten_US
dc.contributor.bilkentauthorDemir, Emek
dc.contributor.bilkentauthorBabur, Özgün
dc.contributor.bilkentauthorDoğrusöz, Uğur
dc.contributor.bilkentauthorGürsoy, Atilla
dc.contributor.bilkentauthorNişancı, Gürkan
dc.contributor.bilkentauthorÇetin Atalay, Rengül
dc.contributor.bilkentauthorÖztürk, Mehmet
dc.date.accessioned2016-02-08T10:32:31Z
dc.date.available2016-02-08T10:32:31Zen_US
dc.date.issued2002-06en_US
dc.departmentDepartment of Molecular Biology and Geneticsen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.departmentBilkent Center for Bioinformatics (BCBI)
dc.description.abstractMotivation: 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.en_US
dc.identifier.doi10.1093/bioinformatics/18.7.996en_US
dc.identifier.eissn1367-4811
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/11693/24660en_US
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttps://doi.org/10.1093/bioinformatics/18.7.996en_US
dc.source.titleBioinformaticsen_US
dc.subjectAutomationen_US
dc.subjectCell functionen_US
dc.subjectComputer graphicsen_US
dc.subjectComputer interfaceen_US
dc.subjectComputer programen_US
dc.subjectControlled studyen_US
dc.subjectData analysisen_US
dc.subjectDNA microarrayen_US
dc.subjectFactual databaseen_US
dc.subjectGene functionen_US
dc.subjectGene identificationen_US
dc.subjectGene sequenceen_US
dc.subjectGenomeen_US
dc.subjectInformation processingen_US
dc.subjectInformation retrievalen_US
dc.subjectMolecular Biologyen_US
dc.subjectPriority journalen_US
dc.subjectProteomicsen_US
dc.subjectCell Physiologyen_US
dc.subjectDatabase Management Systemsen_US
dc.subjectDatabasesen_US
dc.subjectInformation storage and retrievalen_US
dc.subjectInterneten_US
dc.subjectSoftware designen_US
dc.subjectUser-computer interfaceen_US
dc.titlePATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathwaysen_US
dc.typeArticleen_US
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