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Is a SPARQL Endpoint a Good Way to Manage Nursing Documentation

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Is a SPARQL Endpoint a Good Way to Manage Nursing Documentation Is a SPARQL Endpoint a Good way to Manage Nursing Documentation Is a SPARQL Endpoint a good way to Manage Nursing Documentation by Muhammad Aslam Supervisor: Associate Professor Jan Pettersen Nytun Project report for Master Thesis in Information & Communication Technology IKT 590 in Spring 2014 University of Agder Faculty of Engineering and Science Grimstad, 2 June 2014 Status: Final Keywords: Semantic Web, Ontology, Jena, SPARQL, Triple Store, Relational Database Page 1 of 86 Is a SPARQL Endpoint a Good way to Manage Nursing Documentation Abstract. In Semantic Web there are different technologies available, among these technologies ontologies are considered a basic technology to promote semantic management and activities. An ontology is capable to exhibits a common, shareable and reusable view of a specific application domain, and they give meaning to information structures that are exchanged by information systems [63]. In this project our main goal is to develop an application that helps to store and manage the patient related clinical data. For this reason first we made an ontology, in ontology we add some patient related records. After that we made a Java application in which we read this ontology by the help of Jena. Then we checked this application with some other database solutions such as Triple Store (Jena TDB) and Relational database (Jena SDB). After that we performed SPARQL Queries to get results that reads from databases we have used, on the basis of results that we received after performing SPARQL Queries, we made an analysis on the performance and efficiency of databases. In these results we found that Triple Stores (Jena TDB) have capabilities to response very fast among other databases. In this report we also try to present an idea about [62] load times of other native triple stores and discuss the inferencing capabilities of Sesame native, Mulgara and Virtuoso backed with Jena [62]. In this [62] also discuss the suitability and performance of the triple store when used as a backend for Bioportal. Page 2 of 86 Is a SPARQL Endpoint a Good way to Manage Nursing Documentation Preface This report is the final result of a 30 credits Master Thesis, IKT590, completed at the Faculty of Engineering and Science, University of Agder (UiA) in Grimstad, Norway. The work on this project started from 10th January 2014 and ended on 30th May 2014. The main goal of our project is, “Is a SPARQL endpoint a good way to manage nursing documentation”. I am really very obliged to thank our university supervisor, Associate Professor Jan Pettersen Nytun for his constructive support and supervision throughout my thesis without which it would have been really difficult to achieve my goals. His timely feedbacks helped me correcting my mistakes and improving the thesis. I am again very thankful to him for his assistance during meetings at University of Agder. I am also grateful to my family and friends back in Pakistan, specially my parents to support me to study at the University of Agder. Muhammad Aslam University of Agder, Grimstad, Norway June 2nd , 2014 Page 3 of 86 Is a SPARQL Endpoint a Good way to Manage Nursing Documentation Contents 1 Introduction .............................................................................................................. 10 1.1 Background ......................................................................................................... 11 1.1.1 Purpose of Semantic Web. ....................................................................... 11 1.1.2 Limitations on Today’s Web. ..................................................................... 12 1.1.3 Solution by Semantic Web. ....................................................................... 14 1.1.4 Example Application about Semantic Web. .............................................. 14 1.2 Problem statement .............................................................................................. 15 1.3 Literature review .................................................................................................. 16 1.3.1 Correct and professional use of nursing terminology in nursing Documentation16 1.3.2 Purposes of Documentation...................................................................... 16 1.3.3 Systems of documentation ....................................................................... 18 1.4 Problem solution .................................................................................................. 19 1.5 Report outline ...................................................................................................... 20 2 Theoretical background............................................................................................ 21 2.1 Technologies in Semantic Web ............................................................................ 21 2.2 Terminologies Used. ............................................................................................. 23 2.2.1 What is an Ontology? ................................................................................ 24 2.2.2 What is Protégé? ....................................................................................... 26 2.2.3 Ontology Terminologies. ............................................................................ 26 2.2.3.1 What is a Class. ......................................................................... 27 2.2.3.2 What is an Individual (Object). .................................................... 27 2.2.3.3 SubClasses and SuperClasses. .................................................. 27 2.2.3.4 Object Property. .......................................................................... 27 2.2.3.5 Datatype ......................................................................................28 2.2.3.6 Datatype Property ........................................................................28 2.2.3.7 Difference of a Relation and a Property .......................................28 2.2.3.8 Description Logic. ....................................................................... 28 2.3 SPARQL. ............................................................................................................ 29 2.3.1 SPARQL Query .........................................................................................29 2.3.2 Types of SPARQL Queries. ...................................................................... 29 2.3.3 Structure of SPARQL Query. .................................................................... 30 2.4 Jena. ................................................................................................................... 30 2.5 Related Works. .................................................................................................... 31 3 Application Desing ................................................................................................... 34 3.1 Requirements for SPARQL Endpoint Setup ........................................................ 34 3.2 Design Specification for SPARQL Endpoint Setup .............................................. 35 3.2.1 Making Classes in Protégé. ..................................................................... 37 3.2.2 Object Properties for Ontology. ................................................................ 39 3.2.3 Data Properties for Ontology. ................................................................... 41 3.2.4 Instances of Patients as Individual. .......................................................... 43 3.3 Implementation of SPARQL Endpoint. ................................................................. 51 3.3.1 Package Classes for Web Services. ........................................................ 51 3.3.2 Package Classes for Application. ............................................................. 54 3.4 Results on SPARQL Endpoint ............................................................................. 64 3.4.1 SPARQL Queries and their Results ......................................................... 65 3.5 Comparison of other Native Triple Stores ............................................................ 74 3.5.1 Data Sets ................................................................................................. 74 3.5.2 Ontologies from Bioportal ........................................................................ 75 Page 4 of 86 Is a SPARQL Endpoint a Good way to Manage Nursing Documentation 3.5.3 Eveluation Methodology. ......................................................................... 75 3.5.4 Inferencing Approach ............................................................................... 76 3.5.5 Query Results .......................................................................................... 77 3.5.6 Child Queries ........................................................................................... 77 3.5.7 Parent Queries ........................................................................................ 78 3.5.8 Results of Native Triple Stores ................................................................ 79 4 Discussion ............................................................................................................... 81 5 Conclusion ............................................................................................................... 82 References ....................................................................................................................... 83 Page 5 of 86 Is a SPARQL Endpoint a
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