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dc.contributor.advisorDoğrusöz, Uğuren_US
dc.contributor.authorKaraca, Mustafa Enesen_US
dc.date.accessioned2019-02-20T13:39:25Z
dc.date.available2019-02-20T13:39:25Z
dc.date.copyright2019-02
dc.date.issued2019-02
dc.date.submitted2019-02-19
dc.identifier.urihttp://hdl.handle.net/11693/49624
dc.descriptionCataloged from PDF version of article.en_US
dc.descriptionThesis (M.S.): Bilkent University, Department of Computer Engineering, İhsan Doğramacı Bilkent University, 2019.en_US
dc.descriptionIncludes bibliographical references (leaves 61-63).en_US
dc.description.abstractGraph visualization is an important research area that endeavors to make graphs more understandable and easier to analyze. In various domains, graph visualization techniques and standards are developed to effectively analyze underlying graph based data. Systems Biology Graphical Notation (SBGN) is a standard language for modeling biological processes and pathways through graph visualization. Information about SBGN maps can be stored in XML based SBGNML files. libSBGN is a Java/C++ library for reading, writing SBGN-ML and manipulating SBGN maps in an object-oriented manner. Graph databases store data in terms of a graph structure consisting nodes and their relationships. Performing a computation on graph data stored in a graph database by traversals is more e cient than accessing tabled data in relational databases through costly join operations. Neo4j is a prominent graph database that provides a proprietary language named Cypher for querying stored graph data. Neo4j allows writing user defined procedures in Java as plugins to improve capabilities of Neo4j with third party Java libraries. With this thesis, we enable modeling SBGN maps in Neo4j graph database with support for compound structures. Using this SBGN data model in Neo4j, we developed graph based user defined procedures in Java using libSBGN as a plugin to Neo4j. These procedures were used to implement graph query algorithms, such as neighborhood, common stream, and paths between, along with helper functions such as populating a database from an SBGN map and loading an SBGN map from a graph database. These user defined procedures are designed to produce or consume SBGN-ML; hence, they can be used by any visualization tool which can import/export SBGN-ML text. Newt, a web based editor for viewing and diting SBGN maps, is such a tool making use of these procedures and hosting a local Neo4j instance by providing a web service to execute Cypher statements.en_US
dc.description.statementofresponsibilityby Mustafa Enes Karacaen_US
dc.format.extentxv, 63 leaves : illustrations, charts (some color) ; 30 cm.en_US
dc.language.isoEnglishen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectGraph algorithmsen_US
dc.subjectGraph visualizationen_US
dc.subjectSystems biologyen_US
dc.subjectGraph databasesen_US
dc.subjectGraph queryen_US
dc.subjectSBGNen_US
dc.subjectNeo4jen_US
dc.subjectCypheren_US
dc.subjectNewten_US
dc.subjectlibSBGNen_US
dc.subjectSBGN-MLen_US
dc.titleEfficient querying of SBGN maps stored in a graph databaseen_US
dc.title.alternativeÇizge veri tabanında depolanan SBGN haritalarının etkili sorgulanmasıen_US
dc.typeThesisen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.publisherBilkent Universityen_US
dc.description.degreeM.S.en_US
dc.identifier.itemidB159706


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