scholarly journals Enabling Ontology Based Semantic Queries in Biomedical Database Systems

2014 ◽  
Vol 08 (01) ◽  
pp. 67-83 ◽  
Author(s):  
Shuai Zheng ◽  
Fusheng Wang ◽  
James Lu
Keyword(s):  
High Efficiency ◽  
Middle Layer ◽  
Database Systems ◽  
Query Languages ◽  
Database Management System ◽  
Performance Study ◽  
Database Query ◽  
Fully Integrated ◽  
Semantic Query ◽  
Ontology Repository

There is a lack of tools to ease the integration and ontology based semantic queries in biomedical databases, which are often annotated with ontology concepts. We aim to provide a middle layer between ontology repositories and semantically annotated databases to support semantic queries directly in the databases with expressive standard database query languages. We have developed a semantic query engine that provides semantic reasoning and query processing, and translates the queries into ontology repository operations on NCBO BioPortal. Semantic operators are implemented in the database as user defined functions extended to the database engine, thus semantic queries can be directly specified in standard database query languages such as SQL and XQuery. The system provides caching management to boosts query performance. The system is highly adaptable to support different ontologies through easy customizations. We have implemented the system DBOntoLink as an open source software, which supports major ontologies hosted at BioPortal. DBOntoLink supports a set of common ontology based semantic operations and have them fully integrated with a database management system IBM DB2. The system has been deployed and evaluated with an existing biomedical database for managing and querying image annotations and markups (AIM). Our performance study demonstrates the high expressiveness of semantic queries and the high efficiency of the queries.

Database query languages and functional logic programming

2006 ◽  
Vol 24 (2) ◽  
pp. 129-184
Author(s):  
Jesús M. Almendros-Jiménez ◽  
Antonio Becerra-Terón
Keyword(s):  
Logic Programming ◽  
Query Languages ◽  
Database Query ◽  
Functional Logic Programming ◽  
Functional Logic

WATER QUALITY MODELLING WITHIN THE RAISON EXPERT SYSTEM

1994 ◽  
Vol 02 (04) ◽  
pp. 453-466 ◽  
Author(s):  
W.G. BOOTY ◽  
I.W.S. WONG
Keyword(s):  
Water Quality ◽  
Expert System ◽  
Intelligent Systems ◽  
Regional Analysis ◽  
Auxiliary Information ◽  
Database Management System ◽  
Environmental Data ◽  
Microcomputer System ◽  
Analysis Tool ◽  
Fully Integrated

The RAISON (Regional Analysis by Intelligent Systems ON a microcomputer) system is a multimedia environmental data analysis tool-kit that contains a fully integrated database management system, spreadsheet, G.I.S., graphics, statistics, modelling and expert system modules as well as a programming language that allows the user to create specialized applications. This paper presents case studies of modelling applications which illustrate the utility of the system in assisting the users of water quality models to make the models more user friendly. This is accomplished through the use of added visualization of inputs and auxiliary information as well as on-line knowledge added. This system also enables the user to represent model results in numerous graphical forms as well as animated results presented on maps. In addition, it has the ability to interface models with expert systems to aid in the selection and use of models and in the interpretation of results.

Fuzzy XQuery

2015 ◽  
pp. 158-198
Author(s):  
José Ángel Labbad ◽  
Ricardo R. Monascal ◽  
Leonid Tineo
Keyword(s):  
Performance Analysis ◽  
Open Source ◽  
Set Theory ◽  
Fuzzy Set ◽  
Fuzzy Set Theory ◽  
Database Systems ◽  
Query Languages ◽  
Xml Data ◽  
Fuzzy Query ◽  
Query Engine

Traditional database systems and languages are very rigid. XML data and query languages are not the exception. Fuzzy set theory is an appropriate tool for solving this problem. In this sense, Fuzzy XQuery was proposed as an extension of the XQUERY standard. This language defines the xs:truth datatype, the xml:truth attribute and allows the definition and use of fuzzy terms in queries. The main goal of this chapter is to show a high coupling implementation of Fuzzy XQuery within eXist-db, an open source XML DBMS. This extension strategy could also be used with other similar tools. This chapter also presents a statistical performance analysis of the extended fuzzy query engine using the XMark benchmark with user defined fuzzy terms. The study presents promising results.

The Impact of Big Data on Security

Big Data ◽  
2016 ◽  
pp. 1495-1518
Author(s):  
Mohammad Alaa Hussain Al-Hamami
Keyword(s):  
Social Media ◽  
Big Data ◽  
Management System ◽  
Database Management ◽  
Database Systems ◽  
Structured Data ◽  
Database Management System ◽  
Unstructured Data ◽  
And Behavior ◽  
The Impact

Big Data is comprised systems, to remain competitive by techniques emerging due to Big Data. Big Data includes structured data, semi-structured and unstructured. Structured data are those data formatted for use in a database management system. Semi-structured and unstructured data include all types of unformatted data including multimedia and social media content. Among practitioners and applied researchers, the reaction to data available through blogs, Twitter, Facebook, or other social media can be described as a “data rush” promising new insights about consumers' choices and behavior and many other issues. In the past Big Data has been used just by very large organizations, governments and large enterprises that have the ability to create its own infrastructure for hosting and mining large amounts of data. This chapter will show the requirements for the Big Data environments to be protected using the same rigorous security strategies applied to traditional database systems.

Implementation Techniques for Extensible Object Storage Systems

2011 ◽  
pp. 104-127
Author(s):  
Jung-Ho Ahn ◽  
Ha-Joo Song ◽  
Hyoung-Joo Kim
Keyword(s):  
High Performance ◽  
Storage System ◽  
Object Oriented ◽  
Middle Layer ◽  
Database Systems ◽  
Object Oriented Design ◽  
Design And Implementation ◽  
Pointer Swizzling ◽  
Implementation Techniques ◽  
Object Storage

An efficient object manager, a middle layer on top of a storage system, is essential to ensure acceptable performance of object-oriented database systems, since a traditional record-based storage system is too simple to provide object abstraction. In this chapter, we design and implement an extensible object storage system, called Soprano, in an object-oriented fashion which has shown great potential in extensibility and code reusability. Soprano provides a uniform object abstraction and gives us the convenience of persistent programming through many useful persistent classes. Also, Soprano supports efficient object management and pointer swizzling for fast object access. This chapter investigates several aspects of the design and implementation of the extensible object storage system. Our experience shows the feasibility of using an object-oriented design and implementation in building an object storage system that should have both extensibility and high performance.

A Semantic Web-Based Approach for Building Personalized News Services

2011 ◽  
pp. 503-521
Author(s):  
Flavius Frasincar ◽  
Jethro Borsje ◽  
Leonard Levering
Keyword(s):  
Semantic Web ◽  
Language Processing ◽  
Word Sense Disambiguation ◽  
Query Languages ◽  
Word Sense ◽  
Web Based ◽  
Semantic Query ◽  
Web Standards ◽  
Processing Techniques ◽  
News Services

This article proposes Hermes, a Semantic Webbased framework for building personalized news services. It makes use of ontologies for knowledge representation, natural language processing techniques for semantic text analysis, and semantic query languages for specifying wanted information. Hermes is supported by an implementation of the framework, the Hermes News Portal, a tool which allows users to have a personalized online access to news items. The Hermes framework and its associated implementation aim at advancing the state-of-the-art of semantic approaches for personalized news services by employing Semantic Web standards, exploiting domain information, using a word sense disambiguation procedure, and being able to express temporal constraints for the desired news items.

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