Towards an ontology modeling tool. A validation in software engineering scenarios.

Ontology creation and management related processes are very important to define and develop semantic services. Ontology Engineering is the research field that provides the mechanisms to manage the life cycle of the ontologies. However, the process of building ontologies can be tedious and sometimes exhaustive. OWL VisMod is a tool designed for developing ontological engineering based on visual analytics concep tual modeling for OWL ontologies life cycle management, supporting both creation and understanding tasks. This paper is devoted to evaluate OWL VisMod through a set of defined tasks. The same tasks also will be done with the most known tool in Ontology Engineering, Protégé, in order to compare the obtained results and be able to know how is OWL VisMod perceived for the expert users. The comparison shows that both tools have similar acceptation scores, but OWL VisMod presents better feelings regard ing user’s perception tasks due to the visual analytics influence

Using OWL-VisMod through a decision-making process for reusing OWL ontologies

[EN] Knowledge representation (KR) can be defined as a set of ontological commitments, provided with the capabilities of performing inference. The knowledge can be represented using an ontology, which provides a shared insight into a certain domain. The use of ontologies to represent knowledge also allows interoperation among knowledge-based systems. The process of building ontologies can be tedious and sometimes exhaustive. A possible solution in order to avoid this problem would be to reuse the ontologies previously created by others. This paper describes a case study of reusability using OWL-VisMod, a tool designed for developing ontological engineering based on visual conceptual modelling for OWL ontologies. A workflow performed with OWL-VisMod is described; including a decision-making process in order to decide whether or not it could be desirable to reuse an ontology, according to the requirements of a certain project

Ontology driven multi-agent systems : an architecture for sensor web applications.

Thesis (Ph.D.)-University of KwaZulu-Natal, 2009.Advances in sensor technology and space science have resulted in the availability of vast quantities of high quality earth observation data. This data can be used for monitoring the earth and to enhance our understanding of natural processes. Sensor Web researchers are working on constructing a worldwide computing infrastructure that enables dynamic sharing and analysis of complex heterogeneous earth observation data sets. Key challenges that are currently being investigated include data integration; service discovery, reuse and composition; semantic interoperability; and system dynamism. Two emerging technologies that have shown promise in dealing with these challenges are ontologies and software agents. This research investigates how these technologies can be integrated into an Ontology Driven Multi-Agent System (ODMAS) for the Sensor Web. The research proposes an ODMAS framework and an implemented middleware platform, i.e. the Sensor Web Agent Platform (SWAP). SWAP deals with ontology construction, ontology use, and agent based design, implementation and deployment. It provides a semantic infrastructure, an abstract architecture, an internal agent architecture and a Multi-Agent System (MAS) middleware platform. Distinguishing features include: the incorporation of Bayesian Networks to represent and reason about uncertain knowledge; ontologies to describe system entities such as agent services, interaction protocols and agent workflows; and a flexible adapter based MAS platform that facilitates agent development, execution and deployment. SWAP aims to guide and ease the design, development and deployment of dynamic alerting and monitoring applications. The efficacy of SWAP is demonstrated by two satellite image processing applications, viz. wildfire detection and monitoring informal settlement. This approach can provide significant benefits to a wide range of Sensor Web users. These include: developers for deploying agents and agent based applications; end users for accessing, managing and visualising information provided by real time monitoring applications, and scientists who can use the Sensor Web as a scientific computing platform to facilitate knowledge sharing and discovery. An Ontology Driven Multi-Agent Sensor Web has the potential to forever change the way in which geospatial data and knowledge is accessed and used. This research describes this far reaching vision, identifies key challenges and provides a first step towards the vision

Visualisation of Linked Data – Reprise

Linked Data promises to serve as a disruptor of traditional approaches to data management and use, promoting the push from the traditional Web of documents to a Web of data. The ability for data consumers to adopt a follow your nose approach, traversing links defined within a dataset or across independently-curated datasets, is an essential feature of this new Web of Data, enabling richer knowledge retrieval thanks to synthesis across multiple sources of, and views on, inter-related datasets. But for the Web of Data to be successful, we must design novel ways of interacting with the corresponding very large amounts of complex, interlinked, multi-dimensional data throughout its management cycle. The design of user interfaces for Linked Data, and more specifically interfaces that represent the data visually, play a central role in this respect. Contributions to this special issue on Linked Data visualisation investigate different approaches to harnessing visualisation as a tool for exploratory discovery and basic-to-advanced analysis. The papers in this volume illustrate the design and construction of intuitive means for end-users to obtain new insight and gather more knowledge, as they follow links defined across datasets over the Web of Data

Ontology-Driven, Guided Visualisation Supporting Explicit and Composable Mappings

Data masses on the World Wide Web can hardly be managed by humans or machines. One option is the formal description and linking of data sources using Semantic Web and Linked Data technologies. Ontologies written in standardised languages foster the sharing and linking of data as they provide a means to formally define concepts and relations between these concepts. A second option is visualisation. The visual representation allows humans to perceive information more directly, using the highly developed visual sense. Relatively few efforts have been made on combining both options, although the formality and rich semantics of ontological data make it an ideal candidate for visualisation. Advanced visualisation design systems support the visualisation of tabular, typically statistical data. However, visualisations of ontological data still have to be created manually, since automated solutions are often limited to generic lists or node-link diagrams. Also, the semantics of ontological data are not exploited for guiding users through visualisation tasks. Finally, once a good visualisation setting has been created, it cannot easily be reused and shared. Trying to tackle these problems, we had to answer how to define composable and shareable mappings from ontological data to visual means and how to guide the visual mapping of ontological data. We present an approach that allows for the guided visualisation of ontological data, the creation of effective graphics and the reuse of visualisation settings. Instead of generic graphics, we aim at tailor-made graphics, produced using the whole palette of visual means in a flexible, bottom-up approach. It not only allows for visualising ontologies, but uses ontologies to guide users when visualising data and to drive the visualisation process at various places: First, as a rich source of information on data characteristics, second, as a means to formally describe the vocabulary for building abstract graphics, and third, as a knowledge base of facts on visualisation. This is why we call our approach ontology-driven. We suggest generating an Abstract Visual Model (AVM) to represent and »synthesise« a graphic following a role-based approach, inspired by the one used by J. v. Engelhardt for the analysis of graphics. It consists of graphic objects and relations formalised in the Visualisation Ontology (VISO). A mappings model, based on the declarative RDFS/OWL Visualisation Language (RVL), determines a set of transformations from the domain data to the AVM. RVL allows for composable visual mappings that can be shared and reused across platforms. To guide the user, for example, we discourage the construction of mappings that are suboptimal according to an effectiveness ranking formalised in the fact base and suggest more effective mappings instead. The guidance process is flexible, since it is based on exchangeable rules. VISO, RVL and the AVM are additional contributions of this thesis. Further, we initially analysed the state of the art in visualisation and RDF-presentation comparing 10 approaches by 29 criteria. Our approach is unique because it combines ontology-driven guidance with composable visual mappings. Finally, we compare three prototypes covering the essential parts of our approach to show its feasibility. We show how the mapping process can be supported by tools displaying warning messages for non-optimal visual mappings, e.g., by considering relation characteristics such as »symmetry«. In a constructive evaluation, we challenge both the RVL language and the latest prototype trying to regenerate sketches of graphics we created manually during analysis. We demonstrate how graphics can be varied and complex mappings can be composed from simple ones. Two thirds of the sketches can be almost or completely specified and half of them can be almost or completely implemented.:Legend and Overview of Prefixes xiii 1 Introduction 1 2 Background 11 2.1 Visualisation 11 2.1.1 What is Visualisation? 11 2.1.2 What are the Benefits of Visualisation? 12 2.1.3 Visualisation Related Terms Used in this Thesis 12 2.1.4 Visualisation Models and Architectural Patterns 12 2.1.5 Visualisation Design Systems 14 2.1.6 What is the Difference between Visual Mapping and Styling? 14 2.1.7 Lessons Learned from Style Sheet Languages 15 2.2 Data 16 2.2.1 Data – Information – Knowledge 17 2.2.2 Structured Data 17 2.2.3 Ontologies in Computer Science 19 2.2.4 The Semantic Web and its Languages 19 2.2.5 Linked Data and Open Data 20 2.2.6 The Metamodelling Technological Space 21 2.2.7 SPIN 21 2.3 Guidance 22 2.3.1 Guidance in Visualisation 22 3 Problem Analysis 23 3.1 Problems of Ontology Visualisation Approaches 24 3.2 Research Questions 25 3.3 Set up of the Case Studies 25 3.3.1 Case Studies in the Life Sciences Domain 26 3.3.2 Case Studies in the Publishing Domain 26 3.3.3 Case Studies in the Software Technology Domain 27 3.4 Analysis of the Case Studies’ Ontologies 27 3.5 Manual Sketching of Graphics 29 3.6 Analysis of the Graphics for Typical Visualisation Cases 29 3.7 Requirements 33 3.7.1 Requirements for Visualisation and Interaction 34 3.7.2 Requirements for Data Awareness 34 3.7.3 Requirements for Reuse and Composition 34 3.7.4 Requirements for Variability 35 3.7.5 Requirements for Tooling Support and Guidance 35 3.7.6 Optional Features and Limitations 36 4 Analysis of the State of the Art 37 4.1 Related Visualisation Approaches 38 4.1.1 Short Overview of the Approaches 38 4.1.2 Detailed Comparison by Criteria 46 4.1.3 Conclusion – What Is Still Missing? 60 4.2 Visualisation Languages 62 4.2.1 Short Overview of the Compared Languages 62 4.2.2 Detailed Comparison by Language Criteria 66 4.2.3 Conclusion – What Is Still Missing? 71 4.3 RDF Presentation Languages 72 4.3.1 Short Overview of the Compared Languages 72 4.3.2 Detailed Comparison by Language Criteria 76 4.3.3 Additional Criteria for RDF Display Languages 87 4.3.4 Conclusion – What Is Still Missing? 89 4.4 Model-Driven Interfaces 90 4.4.1 Metamodel-Driven Interfaces 90 4.4.2 Ontology-Driven Interfaces 92 4.4.3 Combined Usage of the Metamodelling and Ontology Technological Space 94 5 A Visualisation Ontology – VISO 97 5.1 Methodology Used for Ontology Creation 100 5.2 Requirements for a Visualisation Ontology 100 5.3 Existing Approaches to Modelling in the Field of Visualisation 101 5.3.1 Terminologies and Taxonomies 101 5.3.2 Existing Visualisation Ontologies 102 5.3.3 Other Visualisation Models and Approaches to Formalisation 103 5.3.4 Summary 103 5.4 Technical Aspects of VISO 103 5.5 VISO/graphic Module – Graphic Vocabulary 104 5.5.1 Graphic Representations and Graphic Objects 105 5.5.2 Graphic Relations and Syntactic Structures 107 5.6 VISO/data Module – Characterising Data 110 5.6.1 Data Structure and Characteristics of Relations 110 5.6.2 The Scale of Measurement and Units 112 5.6.3 Properties for Characterising Data Variables in Statistical Data 113 5.7 VISO/facts Module – Facts for Vis. Constraints and Rules 115 5.7.1 Expressiveness of Graphic Relations 116 5.7.2 Effectiveness Ranking of Graphic Relations 118 5.7.3 Rules for Composing Graphics 119 5.7.4 Other Rules to Consider for Visual Mapping 124 5.7.5 Providing Named Value Collections 124 5.7.6 Existing Approaches to the Formalisation of Visualisation Knowledge . . 126 5.7.7 The VISO/facts/empiric Example Knowledge Base 126 5.8 Other VISO Modules 126 5.9 Conclusions and Future Work 127 5.10 Further Use Cases for VISO 127 5.11 VISO on the Web – Sharing the Vocabulary to Build a Community 128 6 A VISO-Based Abstract Visual Model – AVM 129 6.1 Graphical Notation Used in this Chapter 129 6.2 Elementary Graphic Objects and Graphic Attributes 131 6.3 N-Ary Relations 131 6.4 Binary Relations 131 6.5 Composition of Graphic Objects Using Roles 132 6.6 Composition of Graphic Relations Using Roles 132 6.7 Composition of Visual Mappings Using the AVM 135 6.8 Tracing 135 6.9 Is it Worth Having an Abstract Visual Model? 135 6.10 Discussion of Fresnel as a Related Language 137 6.11 Related Work 139 6.12 Limitations 139 6.13 Conclusions 140 7 A Language for RDFS/OWL Visualisation – RVL 141 7.1 Language Requirements 142 7.2 Main RVL Constructs 145 7.2.1 Mapping 145 7.2.2 Property Mapping 146 7.2.3 Identity Mapping 146 7.2.4 Value Mapping 147 7.2.5 Inheriting RVL Settings 147 7.2.6 Resource Mapping 148 7.2.7 Simplifications 149 7.3 Calculating Value Mappings 150 7.4 Defining Scale of Measurement 153 7.4.1 Determining the Scale of Measurement 154 7.5 Addressing Values in Value Mappings 156 7.5.1 Determining the Set of Addressed Source Values 156 7.5.2 Determining the Set of Addressed Target Values 157 7.6 Overlapping Value Mappings 158 7.7 Default Value Mapping 158 7.8 Default Labelling 159 7.9 Defining Interaction 159 7.10 Mapping Composition and Submappings 160 7.11 A Schema Language for RVL 160 7.11.1 Concrete Examples of the RVL Schema 163 7.12 Conclusions and Future Work 166 8 The OGVIC Approach 169 8.1 Ontology-Driven, Guided Editing of Visual Mappings 172 8.1.1 Classification of Constraints 172 8.1.2 Levels of Guidance 173 8.1.3 Implementing Constraint-Based Guidance 173 8.2 Support of Explicit and Composable Visual Mappings 177 8.2.1 Mapping Composition Cases 178 8.2.2 Selecting a Context 180 8.2.3 Using the Same Graphic Relation Multiple Times 181 8.3 Prototype P1 (TopBraid-Composer-based) 182 8.4 Prototype P2 (OntoWiki-based) 184 8.5 Prototype P3 (Java Implementation of RVL) 187 8.6 Lessons Learned from Prototypes & Future Work 190 8.6.1 Checking RVL Constraints and Visualisation Rules 190 8.6.2 A User Interface for Editing RVL Mappings 190 8.6.3 Graph Transformations with SPIN and SPARQL 1.1 Update 192 8.6.4 Selection and Filtering of Data 193 8.6.5 Interactivity and Incremental Processing 193 8.6.6 Rendering the Final Platform-Specific Code 196 9 Application 197 9.1 Coverage of Case Study Sketches and Necessary Features 198 9.2 Coverage of Visualisation Cases 201 9.3 Coverage of Requirements 205 9.4 Full Example 206 10 Conclusions 211 10.1 Contributions 211 10.2 Constructive Evaluation 212 10.3 Research Questions 213 10.4 Transfer to Other Models and Constraint Languages 213 10.5 Limitations 214 10.6 Future Work 214 Appendices 217 A Case Study Sketches 219 B VISO – Comparison of Visualisation Literature 229 C RVL 231 D RVL Example Mappings and Application 233 D.1 Listings of RVL Example Mappings as Required by Prototype P3 233 D.2 Features Required for Implementing all Sketches 235 D.3 JSON Format for Processing the AVM with D3 – Hierarchical Variant 238 Bibliography 238 List of Figures 251 List of Tables 254 List of Listings 257Datenmassen im World Wide Web können kaum von Menschen oder Maschinen erfasst werden. Eine Option ist die formale Beschreibung und Verknüpfung von Datenquellen mit Semantic-Web- und Linked-Data-Technologien. Ontologien, in standardisierten Sprachen geschrieben, befördern das Teilen und Verknüpfen von Daten, da sie ein Mittel zur formalen Definition von Konzepten und Beziehungen zwischen diesen Konzepten darstellen. Eine zweite Option ist die Visualisierung. Die visuelle Repräsentation ermöglicht es dem Menschen, Informationen direkter wahrzunehmen, indem er seinen hochentwickelten Sehsinn verwendet. Relativ wenige Anstrengungen wurden unternommen, um beide Optionen zu kombinieren, obwohl die Formalität und die reichhaltige Semantik ontologische Daten zu einem idealen Kandidaten für die Visualisierung machen. Visualisierungsdesignsysteme unterstützen Nutzer bei der Visualisierung von tabellarischen, typischerweise statistischen Daten. Visualisierungen ontologischer Daten jedoch müssen noch manuell erstellt werden, da automatisierte Lösungen häufig auf generische Listendarstellungen oder Knoten-Kanten-Diagramme beschränkt sind. Auch die Semantik der ontologischen Daten wird nicht ausgenutzt, um Benutzer durch Visualisierungsaufgaben zu führen. Einmal erstellte Visualisierungseinstellungen können nicht einfach wiederverwendet und geteilt werden. Um diese Probleme zu lösen, mussten wir eine Antwort darauf finden, wie die Definition komponierbarer und wiederverwendbarer Abbildungen von ontologischen Daten auf visuelle Mittel geschehen könnte und wie Nutzer bei dieser Abbildung geführt werden könnten. Wir stellen einen Ansatz vor, der die geführte Visualisierung von ontologischen Daten, die Erstellung effektiver Grafiken und die Wiederverwendung von Visualisierungseinstellungen ermöglicht. Statt auf generische Grafiken zielt der Ansatz auf maßgeschneiderte Grafiken ab, die mit der gesamten Palette visueller Mittel in einem flexiblen Bottom-Up-Ansatz erstellt werden. Er erlaubt nicht nur die Visualisierung von Ontologien, sondern verwendet auch Ontologien, um Benutzer bei der Visualisierung von Daten zu führen und den Visualisierungsprozess an verschiedenen Stellen zu steuern: Erstens als eine reichhaltige Informationsquelle zu Datencharakteristiken, zweitens als Mittel zur formalen Beschreibung des Vokabulars für den Aufbau von abstrakten Grafiken und drittens als Wissensbasis von Visualisierungsfakten. Deshalb nennen wir unseren Ansatz ontologie-getrieben. Wir schlagen vor, ein Abstract Visual Model (AVM) zu generieren, um eine Grafik rollenbasiert zu synthetisieren, angelehnt an einen Ansatz der von J. v. Engelhardt verwendet wird, um Grafiken zu analysieren. Das AVM besteht aus grafischen Objekten und Relationen, die in der Visualisation Ontology (VISO) formalisiert sind. Ein Mapping-Modell, das auf der deklarativen RDFS/OWL Visualisation Language (RVL) basiert, bestimmt eine Menge von Transformationen von den Quelldaten zum AVM. RVL ermöglicht zusammensetzbare »Mappings«, visuelle Abbildungen, die über Plattformen hinweg geteilt und wiederverwendet werden können. Um den Benutzer zu führen, bewerten wir Mappings anhand eines in der Faktenbasis formalisierten Effektivitätsrankings und schlagen ggf. effektivere Mappings vor. Der Beratungsprozess ist flexibel, da er auf austauschbaren Regeln basiert. VISO, RVL und das AVM sind weitere Beiträge dieser Arbeit. Darüber hinaus analysieren wir zunächst den Stand der Technik in der Visualisierung und RDF-Präsentation, indem wir 10 Ansätze nach 29 Kriterien vergleichen. Unser Ansatz ist einzigartig, da er eine ontologie-getriebene Nutzerführung mit komponierbaren visuellen Mappings vereint. Schließlich vergleichen wir drei Prototypen, welche die wesentlichen Teile unseres Ansatzes umsetzen, um seine Machbarkeit zu zeigen. Wir zeigen, wie der Mapping-Prozess durch Tools unterstützt werden kann, die Warnmeldungen für nicht optimale visuelle Abbildungen anzeigen, z. B. durch Berücksichtigung von Charakteristiken der Relationen wie »Symmetrie«. In einer konstruktiven Evaluation fordern wir sowohl die RVL-Sprache als auch den neuesten Prototyp heraus, indem wir versuchen Skizzen von Grafiken umzusetzen, die wir während der Analyse manuell erstellt haben. Wir zeigen, wie Grafiken variiert werden können und komplexe Mappings aus einfachen zusammengesetzt werden können. Zwei Drittel der Skizzen können fast vollständig oder vollständig spezifiziert werden und die Hälfte kann fast vollständig oder vollständig umgesetzt werden.:Legend and Overview of Prefixes xiii 1 Introduction 1 2 Background 11 2.1 Visualisation 11 2.1.1 What is Visualisation? 11 2.1.2 What are the Benefits of Visualisation? 12 2.1.3 Visualisation Related Terms Used in this Thesis 12 2.1.4 Visualisation Models and Architectural Patterns 12 2.1.5 Visualisation Design Systems 14 2.1.6 What is the Difference between Visual Mapping and Styling? 14 2.1.7 Lessons Learned from Style Sheet Languages 15 2.2 Data 16 2.2.1 Data – Information – Knowledge 17 2.2.2 Structured Data 17 2.2.3 Ontologies in Computer Science 19 2.2.4 The Semantic Web and its Languages 19 2.2.5 Linked Data and Open Data 20 2.2.6 The Metamodelling Technological Space 21 2.2.7 SPIN 21 2.3 Guidance 22 2.3.1 Guidance in Visualisation 22 3 Problem Analysis 23 3.1 Problems of Ontology Visualisation Approaches 24 3.2 Research Questions 25 3.3 Set up of the Case Studies 25 3.3.1 Case Studies in the Life Sciences Domain 26 3.3.2 Case Studies in the Publishing Domain 26 3.3.3 Case Studies in the Software Technology Domain 27 3.4 Analysis of the Case Studies’ Ontologies 27 3.5 Manual Sketching of Graphics 29 3.6 Analysis of the Graphics for Typical Visualisation Cases 29 3.7 Requirements 33 3.7.1 Requirements for Visualisation and Interaction 34 3.7.2 Requirements for Data Awareness 34 3.7.3 Requirements for Reuse and Composition 34 3.7.4 Requirements for Variability 35 3.7.5 Requirements for Tooling Support and Guidance 35 3.7.6 Optional Features and Limitations 36 4 Analysis of the State of the Art 37 4.1 Related Visualisation Approaches 38 4.1.1 Short Overview of the Approaches 38 4.1.2 Detailed Comparison by Criteria 46 4.1.3 Conclusion – What Is Still Missing? 60 4.2 Visualisation Languages 62 4.2.1 Short Overview of the Compared Languages 62 4.2.2 Detailed Comparison by Language Criteria 66 4.2.3 Conclusion – What Is Still Missing? 71 4.3 RDF Presentation Languages 72 4.3.1 Short Overview of the Compared Languages 72 4.3.2 Detailed Comparison by Language Criteria 76 4.3.3 Additional Criteria for RDF Display Languages 87 4.3.4 Conclusion – What Is Still Missing? 89 4.4 Model-Driven Interfaces 90 4.4.1 Metamodel-Driven Interfaces 90 4.4.2 Ontology-Driven Interfaces 92 4.4.3 Combined Usage of the Metamodelling and Ontology Technological Space 94 5 A Visualisation Ontology – VISO 97 5.1 Methodology Used for Ontology Creation 100 5.2 Requirements for a Visualisation Ontology 100 5.3 Existing Approaches to Modelling in the Field of Visualisation 101 5.3.1 Terminologies and Taxonomies 101 5.3.2 Existing Visualisation Ontologies 102 5.3.3 Other Visualisation Models and Approaches to Formalisation 103 5.3.4 Summary 103 5.4 Technical Aspects of VISO 103 5.5 VISO/graphic Module – Graphic Vocabulary 104 5.5.1 Graphic Representations and Graphic Objects 105 5.5.2 Graphic Relations and Syntactic Structures 107 5.6 VISO/data Module – Characterising Data 110 5.6.1 Data Structure and Characteristics of Relations 110 5.6.2 The Scale of Measurement and Units 112 5.6.3 Properties for Characterising Data Variables in Statistical Data 113 5.7 VISO/facts Module – Facts for Vis. Constraints and Rules 115 5.7.1 Expressiveness of Graphic Relations 116 5.7.2 Effectiveness Ranking of Graphic Relations 118 5.7.3 Rules for Composing Graphics 119 5.7.4 Other Rules to Consider for Visual Mapping 124 5.7.5 Providing Named Value Collections 124 5.7.6 Existing Approaches to the Formalisation of Visualisation Knowledge . . 126 5.7.7 The VISO/facts/empiric Example Knowledge Base 126 5.8 Other VISO Modules 126 5.9 Conclusions and Future Work 127 5.10 Further Use Cases for VISO 127 5.11 VISO on the Web – Sharing the Vocabulary to Build a Community 128 6 A VISO-Based Abstract Visual Model – AVM 129 6.1 Graphical Notation Used in this Chapter 129 6.2 Elementary Graphic Objects and Graphic Attributes 131 6.3 N-Ary Relations 131 6.4 Binary Relations 131 6.5 Composition of Graphic Objects Using Roles 132 6.6 Composition of Graphic Relations Using Roles 132 6.7 Composition of Visual Mappings Using the AVM 135 6.8 Tracing 135 6.9 Is it Worth Having an Abstract Visual Model? 135 6.10 Discussion of Fresnel as a Related Language 137 6.11 Related Work 139 6.12 Limitations 139 6.13 Conclusions 140 7 A Language for RDFS/OWL Visualisation – RVL 141 7.1 Language Requirements 142 7.2 Main RVL Constructs 145 7.2.1 Mapping 145 7.2.2 Property Mapping 146 7.2.3 Identity Mapping 146 7.2.4 Value Mapping 147 7.2.5 Inheriting RVL Settings 147 7.2.6 Resource Mapping 148 7.2.7 Simplifications 149 7.3 Calculating Value Mappings 150 7.4 Defining Scale of Measurement 153 7.4.1 Determining the Scale of Measurement 154 7.5 Addressing Values in Value Mappings 156 7.5.1 Determining the Set of Addressed Source Values 156 7.5.2 Determining the Set of Addressed Target Values 157 7.6 Overlapping Value Mappings 158 7.7 Default Value Mapping 158 7.8 Default Labelling 159 7.9 Defining Interaction 159 7.10 Mapping Composition and Submappings 160 7.11 A Schema Language for RVL 160 7.11.1 Concrete Examples of the RVL Schema 163 7.12 Conclusions and Future Work 166 8 The OGVIC Approach 169 8.1 Ontology-Driven, Guided Editing of Visual Mappings 172 8.1.1 Classification of Constraints 172 8.1.2 Levels of Guidance 173 8.1.3 Implementing Constraint-Based Guidance 173 8.2 Support of Explicit and Composable Visual Mappings 177 8.2.1 Mapping Composition Cases 178 8.2.2 Selecting a Context 180 8.2.3 Using the Same Graphic Relation Multiple Times 181 8.3 Prototype P1 (TopBraid-Composer-based) 182 8.4 Prototype P2 (OntoWiki-based) 184 8.5 Prototype P3 (Java Implementation of RVL) 187 8.6 Lessons Learned from Prototypes & Future Work 190 8.6.1 Checking RVL Constraints and Visualisation Rules 190 8.6.2 A User Interface for Editing RVL Mappings 190 8.6.3 Graph Transformations with SPIN and SPARQL 1.1 Update 192 8.6.4 Selection and Filtering of Data 193 8.6.5 Interactivity and Incremental Processing 193 8.6.6 Rendering the Final Platform-Specific Code 196 9 Application 197 9.1 Coverage of Case Study Sketches and Necessary Features 198 9.2 Coverage of Visualisation Cases 201 9.3 Coverage of Requirements 205 9.4 Full Example 206 10 Conclusions 211 10.1 Contributions 211 10.2 Constructive Evaluation 212 10.3 Research Questions 213 10.4 Transfer to Other Models and Constraint Languages 213 10.5 Limitations 214 10.6 Future Work 214 Appendices 217 A Case Study Sketches 219 B VISO – Comparison of Visualisation Literature 229 C RVL 231 D RVL Example Mappings and Application 233 D.1 Listings of RVL Example Mappings as Required by Protot

Scaling the development of large ontologies : identitas and hypernormalization

PhD ThesisDuring the last decade ontologies have become a fundamental part of the life sciences to build organised computational knowledge. Currently, there are more than 800 biomedical ontologies hosted by the NCBO BioPortal repository. However, the proliferation of ontologies in the biomedical and biological domains has highlighted a number of problems. As ontologies become large, their development and maintenance becomes more challenging and time-consuming. Therefore, the scalability of ontology development has become problematic. In this thesis, we examine two new approaches that can help address this challenge. First, we consider a new approach to identi ers that could signi cantly facilitate the scalability of ontologies and overcome some related issues with monotonic, numeric identi ers while remaining semantics-free. Our solutions are described, along with the Identitas library, which allows concurrent development, pronounceability and error checking. The library integrated into two ontology development environments, Prot eg e and Tawny-OWL. This thesis also discusses the ways in which current ontological practices could be migrated towards the use of this scheme. Second, we investigate the usage of the hypernormalisation, patternisation and programatic approaches by asking how we could use this approach to rebuild the Gene Ontology (GO). The aim of the hypernormalisation and patternisation techniques is to allow the ontology developer to manage its maintainability and evolution. To apply this approach we had to analyse the ontology structure, starting with the Molecular Function Ontology (MFO). The MFO is formed from several large and tangled hierarchies of classes, each of which describe a broad molecular activity. The exploitation of the hypernormalisation approach resulted in the creation of a hypernormalised form of the Transporter Activity (TA) and Catalytic Activity (CA) hierarchies, together they constitute 78% of all classes in MFO. The hypernormalised structure of the TA and CA are generated based on developed higher-level patterns and novel content-speci c patterns, and exploit ontology logical reasoners. The gen- erated ontologies are robust, easy to maintain and can be developed and extended freely. Although, there are a variety of ontologies development tools, Tawny-OWL is a programmatic interactive tool for ontology creation and management and provides a set of patterns that explicitly support the creation of a hypernormalised ontology. Finally, the investigation of the hypernormalisation highlighted inconsistent classi- cations and identi cation of signi cant semantic mismatch between GO and the Chemical Entities of Biological Interest (ChEBI). Although both ontologies describe the same real entities, GO often refers to the form most common in biology, while ChEBI is more speci c and precise. The use of hypernormalisation forces us to deal with this mismatch, we used the equivalence axioms created by the GO-Plus ontology. To sum up, to address the scalability and ease development of ontologies we propose a new identi er scheme and investigate the use of the hypernormalisation methodology. Together, the Identitas and the hypernormalisation technique should enable the construction of large-scale ontologies in the future.Northern Borders University, Saudi Arabia

Security-Driven Software Evolution Using A Model Driven Approach

High security level must be guaranteed in applications in order to mitigate risks during the deployment of information systems in open network environments. However, a significant number of legacy systems remain in use which poses security risks to the enterprise’ assets due to the poor technologies used and lack of security concerns when they were in design. Software reengineering is a way out to improve their security levels in a systematic way. Model driven is an approach in which model as defined by its type directs the execution of the process. The aim of this research is to explore how model driven approach can facilitate the software reengineering driven by security demand. The research in this thesis involves the following three phases. Firstly, legacy system understanding is performed using reverse engineering techniques. Task of this phase is to reverse engineer legacy system into UML models, partition the legacy system into subsystems with the help of model slicing technique and detect existing security mechanisms to determine whether or not the provided security in the legacy system satisfies the user’s security objectives. Secondly, security requirements are elicited using risk analysis method. It is the process of analysing key aspects of the legacy systems in terms of security. A new risk assessment method, taking consideration of asset, threat and vulnerability, is proposed and used to elicit the security requirements which will generate the detailed security requirements in the specific format to direct the subsequent security enhancement. Finally, security enhancement for the system is performed using the proposed ontology based security pattern approach. It is the stage that security patterns derived from security expertise and fulfilling the elicited security requirements are selected and integrated in the legacy system models with the help of the proposed security ontology. The proposed approach is evaluated by the selected case study. Based on the analysis, conclusions are drawn and future research is discussed at the end of this thesis. The results show this thesis contributes an effective, reusable and suitable evolution approach for software security

Service-oriented design of environmental information systems

Service-orientation has an increasing impact upon the design process and the architecture of environmental information systems. This thesis specifies the SERVUS design methodology for geospatial applications based upon standards of the Open Geospatial Consortium. SERVUS guides the system architect to rephrase use case requirements as a network of semantically-annotated requested resources and to iteratively match them with offered resources that mirror the capabilities of existing services