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Query Language for Biological Databases
Bahurek, Tomáš ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.
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Java AST Query Language
Bílek, Jiří ; Matula, Peter (referee) ; Křivka, Zbyněk (advisor)
The purpose of this thesis is to design a Java AST query language and implement tool that uses the query language. This work overviews graph databases and their libraries with focus on Neo4J and Titan. This thesis overviews tools Java bytecode analysis as well. Libraries Procyon and BCEL are described in detail. The work includes a proposal the query language and detailed description of the tool implementation, together with the detailed description of the way how Java entities are stored into the graph databases. In the end, the work deals with experiments and the evaluation of the time complexity of the library.
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SPARQL plugin for Ontopia Knowledge Suite
Ovčáčík, Vlastimil ; Kliegr, Tomáš (advisor) ; Svátek, Vojtěch (referee)
Reader of this bachelor thesis will familiarize with two technologies of semantic web -- Topic Maps and RDF. In the first half of this document we can find principles, history and thoughts on near future of both technologies. There are explained necessary principles of both standards. Emphasis is placed on query languages SPARQL and TMQL. Object of this thesis is understanding differences and mutual aspects of both Topic Maps and RDF. This understanding is key for finding interoperability between these two technologies on semantic web. The second half of this thesis is aimed on implementation of sparql4ontopia - a plugin for Ontopia Knowledge Suite, which enables quering topic maps with SPARQL. This plugin utilizes Sesame project for SPARQL query evaluation and Nikunau tool from SesameTM project for mapping SPARQL on Topic Maps Data Model. Possibilities and limitations of this plugin are described. There is also description of sparql4ontopia development and implementation. Last chapter shed light on SPARQL endpoint and possible way of implementation into Ontopia Knowledge Suite.
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