An ontology for collaborative construction and analysis of cellular pathways

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buir.contributor.authorDemir, Emek
buir.contributor.authorBabur, Özgün
buir.contributor.authorDoğrusöz, Uğur
buir.contributor.authorGürsoy, Atilla
buir.contributor.authorAyaz, Aslı
buir.contributor.authorGüleşır, Gürcan
buir.contributor.authorNişancı, Gürkan
buir.contributor.authorÇetin Atalay, Rengül
dc.citation.epage356en_US
dc.citation.issueNumber3en_US
dc.citation.spage349en_US
dc.citation.volumeNumber20en_US
dc.contributor.authorDemir, Emeken_US
dc.contributor.authorBabur, Özgünen_US
dc.contributor.authorDoğrusöz, Uğuren_US
dc.contributor.authorGürsoy, Atillaen_US
dc.contributor.authorAyaz, Aslıen_US
dc.contributor.authorGüleşır, Gürcanen_US
dc.contributor.authorNişancı, Gürkanen_US
dc.contributor.authorÇetin Atalay, Rengülen_US
dc.date.accessioned2016-02-08T10:27:32Z
dc.date.available2016-02-08T10:27:32Zen_US
dc.date.issued2004-02-12en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.departmentDepartment of Molecular Biology and Geneticsen_US
dc.departmentBilkent Center for Bioinformatics (BCBI)
dc.description.abstractMotivation: 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.en_US
dc.identifier.doi10.1093/bioinformatics/btg416en_US
dc.identifier.eissn1367-4811
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/11693/24320en_US
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttp://dx.doi.org/10.1093/bioinformatics/btg416en_US
dc.source.titleBioinformaticsen_US
dc.subjectCell activityen_US
dc.subjectComputer programen_US
dc.subjectControlled studyen_US
dc.subjectFactualen_US
dc.subjectGene functionen_US
dc.subjectGene identificationen_US
dc.subjectGenome analysisen_US
dc.subjectMathematical computingen_US
dc.subjectMolecular interactionen_US
dc.subjectMolecular mechanicsen_US
dc.subjectPriority journalen_US
dc.subjectValidation processen_US
dc.subjectBiopolymersen_US
dc.subjectCell Physiologyen_US
dc.subjectDatabase management systemsen_US
dc.subjectDatabasesen_US
dc.subjectInformation storage and retrievalen_US
dc.subjectModelsen_US
dc.subjectSignal transductionen_US
dc.subjectSoftwareen_US
dc.subjectSystems Iitegrationen_US
dc.subjectUser-computer interfaceen_US
dc.subjectBiologicalen_US
dc.titleAn ontology for collaborative construction and analysis of cellular pathwaysen_US
dc.typeArticleen_US
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Department of Computer Engineering
Bilkent Center for Bioinformatics (BCBI)
Department of Molecular Biology and Genetics