Semantically-enabled applications, such as ontology-based search and data integration, take into account the semantics of the input data in their algorithms. Such applications often use ontologies, which model the application domains in question, as well as alignments, which provide information about the relationships between the terms in the different ontologies. The quality and reliability of the results of such applications depend directly on the correctness and completeness of the ontologies and alignments they utilize. Traditionally, ontology debugging discovers defects in ontologies and alignments and provides means for improving their correctness and completeness, while ontology alignment establishes the relationships between the terms in the different ontologies, thus addressing completeness of alignments. This thesis focuses on the integration of ontology alignment and debugging for taxonomy networks which are formed by taxonomies, the most widely used kind of ontologies, connected through alignments. The contributions of this thesis include the following. To the best of our knowledge, we have developed the first approach and framework that integrate ontology alignment and debugging, and allow debugging of modelling defects both in the structure of the taxonomies as well as in their alignments. As debugging modelling defects requires domain knowledge, we have developed algorithms that employ the domain knowledge intrinsic to the network to detect and repair modelling defects. Further, a system has been implemented and several experiments with real-world ontologies have been performed in order to demonstrate the advantages of our integrated ontology alignment and debugging approach. For instance, in one of the experiments with the well-known ontologies and alignment from the Anatomy track in Ontology Alignment Evaluation Initiative 2010, 203 modelling defects (concerning incomplete and incorrect information) were discovered and repaired.

Knowledge-driven problem solving demands 'complete' knowledge about the domain and its interpretation under different contexts. Knowledge Morphing aims at a context-driven integration of heterogeneous knowledge sources--in order to provide a comprehensive and networked view of all knowledge about a domain-specific problem, pertaining to the context at hand. In this PhD thesis, we have proposed a Semantic Web based framework, K-MORPH, for Knowledge Morphing via Reconciliation of Contextualized Sub-ontologies. In order to realize our K-MORPH framework, we have developed: (i) a sub-ontology extraction method for generating contextualized sub-ontologies from the source ontologies pertinent to the problem-context at hand; (ii) two ontology matching approaches: triple-based ontology matching (TOM) and proof-based ontology matching (POM) for finding both atomic and complex correspondences between two extracted contextualized sub-ontologies; and (iii) our approach for resolving inconsistencies in ontologies by generating minimal inconsistent resolve candidates (MIRCs), where removing any of the MIRCs from the inconsistent ontology results in a maximal consistent sub-ontology. Thus, K-MORPH performs knowledge morphing among ontology-modelled knowledge sources and generates a context-sensitive and comprehensive knowledge-base pertinent to the problem at hand by (a) extracting problem-specific knowledge components from ontology-modelled knowledge sources using our sub-ontology extraction method; (b) aligning and merging the extracted knowledge components using our matching approaches; and (c) repairing inconsistencies in the morphed knowledge by applying our approach for detecting and resolving inconsistencies. We demonstrated the application of our K-MORPH framework in the healthcare domain, where K-MORPH generated a merged ontology for providing a comprehensive therapeutic knowledge-base for Urinary Tract Infections (UTI) by first (i) extracting 20 contextualized sub-ontologies from various UTI ontologies of different healthcare institutions, (ii) aligning and merging the extracted UTI sub-ontologies, and (iii) detecting and resolving inconsistencies in the merged UTI ontology.

With the popularity of the World Wide Web, a large amount of data is generated and made available through the Internet everyday. To integrate and query this huge amount of heterogeneous data, the vision of Semantic Web has been recognized as a possible solution. One key technology for the Semantic Web is ontologies. Many ontologies have been developed in recent years. Meanwhile, due to the demand of applications using multiple ontologies,  mappings between entities of these ontologies are generated as well, which leads to the generation of ontology networks consisting of ontologies and mappings between these ontologies. However, neither developing ontologies nor finding mappings between ontologies is an easy task. It may happen that the ontologies are not consistent or complete, or the mappings between these ontologies are not correct or complete, or the resulting ontology network is not consistent. This may lead to problems when they are used in semantically-enabled applications. In this thesis, we address two issues relevant to the quality of the mappings and the structure in the ontology network. The first issue deals with the missing mappings between networked ontologies. Assuming existing mappings between ontologies are correct, we investigate whether and how to use these existing mappings, to find more mappings between ontologies. We propose and test several strategies of using the given correct mappings to align ontologies. The second issue deals with the missing structure, in particular missing is-a relations, in networked ontologies. Based on the assumption that missing is-a relations are a kind of modeling defects, we propose an ontology debugging approach to tackle this issue. We develop an algorithm for detecting missing is-a relations in ontologies, as well as algorithms which assist the user in repairing by generating and recommending possible ways of repairing and executing the repairing. Based on this approach, we develop a system and test its use and performance.

The World Wide Web contains large amounts of data and in most cases this data is without any explicit structure. The lack of structure makes it difficult for automated agents to understand and use such data. A step towards a more structured World Wide Web is the idea of the Semantic Web which aims at introducing semantics to data on the World Wide Web. One of the key technologies in this endeavour are ontologies which provide means for modeling a domain of interest. Developing and maintaining ontologies is not an easy task and it is often the case that defects are introduced into ontologies. This can be a problem for semantically-enabled applications such as ontology-based querying. Defects in ontologies directly influence the quality of the results of such applications as correct results can be missed and wrong results can be returned. This thesis considers one type of defects in ontologies, namely the problem of completing the is-a structure in ontologies represented in description logics. We focus on two variants of description logics, the EL family and ALC, which are often used in practice. The contributions of this thesis are as follows. First, we formalize the problem of completing the is-a structure as a generalized TBox abduction problem (GTAP) which is a new type of abduction problem in description logics. Next, we provide algorithms for solving GTAP in the EL family and ALC description logics. Finally, we describe two implemented systems based on the introduced algorithms. The systems were evaluated in two experiments which have shown the usefulness of our approach. For example, in one experiment using ontologies from the Ontology Alignment Evaluation Initiative 58 and 94 detected missing is-a relations were repaired by adding 54 and 101 is-a relations, respectively, introducing new knowledge to the ontologies.

The World Wide Web contains large amounts of data, and in most cases this data has no explicit structure. The lack of structure makes it difficult for automated agents to understand and use such data. A step towards a more structured World Wide Web is the Semantic Web, which aims at introducing semantics to data on the World Wide Web. One of the key technologies in this endeavour are ontologies, which provide a means for modeling a domain of interest and are used for search and integration of data. In recent years many ontologies have been developed. To be able to use multiple ontologies it is necessary to align them, i.e., find inter-ontology relationships. However, developing and aligning ontologies is not an easy task and it is often the case that ontologies and their alignments are incorrect and incomplete. This can be a problem for semantically-enabled applications. Incorrect and incomplete ontologies and alignments directly influence the quality of the results of such applications, as wrong results can be returned and correct results can be missed. This thesis focuses on the problem of completing ontologies and ontology networks. The contributions of the thesis are threefold. First, we address the issue of completing the is-a structure and alignment in ontologies and ontology networks. We have formalized the problem of completing the is-a structure in ontologies as an abductive reasoning problem and developed algorithms as well as systems for dealing with the problem. With respect to the completion of alignments, we have studied system performance in the Ontology Alignment Evaluation Initiative, a yearly evaluation campaign for ontology alignment systems. We have also addressed the scalability of ontology matching, which is one of the current challenges, by developing an approach for reducing the search space when generating the alignment.Second, high quality completion requires user involvement. As users' time and effort are a limited resource we address the issue of limiting and facilitating user interaction in the completion process. We have conducted a broad study of state-of-the-art ontology alignment systems and identified different issues related to the process. We have also conducted experiments to assess the impact of user errors in the completion process. While the completion of ontologies and ontology networks can be done at any point in the life-cycle of ontologies and ontology networks, some of the issues can be addressed already in the development phase. The third contribution of the thesis addresses this by introducing ontology completion and ontology alignment into an existing ontology development methodology.

As Lógicas de Descrição são usadas como base para a linguagem OWL, padrão para representação de ontologias na web. No entanto, conhecimento não é estático e, com tal dinamismo, o estudo de revisão de crenças e sua correta e adequada aplicação tornam-se muito importantes. Neste trabalho, pretendemos desenvolver uma ferramenta para revisão de ontologias como um plug-in para o Protégé, o editor de ontologias mais utilizado atualmente. / Description Logics are the basis for OWL language, which is the standard to represent ontologies on the web. However, knowledge is usually not satic and its dynamics brings the importance of belief revision and its correct and proper application. In this work, we intend to develop a tool for revising ontologies as a plug-in for Protégé, the most used ontology editor nowadays.

As Lógicas de Descrição são usadas como base para a linguagem OWL, padrão para representação de ontologias na web. No entanto, conhecimento não é estático e, com tal dinamismo, o estudo de revisão de crenças e sua correta e adequada aplicação tornam-se muito importantes. Neste trabalho, pretendemos desenvolver uma ferramenta para revisão de ontologias como um plug-in para o Protégé, o editor de ontologias mais utilizado atualmente. / Description Logics are the basis for OWL language, which is the standard to represent ontologies on the web. However, knowledge is usually not satic and its dynamics brings the importance of belief revision and its correct and proper application. In this work, we intend to develop a tool for revising ontologies as a plug-in for Protégé, the most used ontology editor nowadays.

The abundance of data at our disposal empowers data-driven applications and decision making. The knowledge captured in the data, however, has not been utilized to full potential, as it is only accessible to human interpretation and data are distributed in heterogeneous repositories. Ontologies are a key technology unlocking the knowledge in the data by providing means to model the world around us and infer knowledge implicitly captured in the data. As data are hosted by independent organizations we often need to use several ontologies and discover the relationships between them in order to support data and knowledge transfer. Broadly speaking, while ontologies provide formal representations and thus the basis, ontology alignment supplies integration techniques and thus the means to turn the data kept in distributed, heterogeneous repositories into valuable knowledge. While many automatic approaches for creating alignments have already been developed, user input is still required for obtaining the highest-quality alignments. This thesis focuses on supporting users during the cognitively intensive alignment process and makes several contributions. We have identified front- and back-end system features that foster user involvement during the alignment process and have investigated their support in existing systems by user interface evaluations and literature studies. We have further narrowed down our investigation to features in connection to the, arguably, most cognitively demanding task from the users’ perspective—manual validation—and have also considered the level of user expertise by assessing the impact of user errors on alignments’ quality. As developing and aligning ontologies is an error-prone task, we have focused on the benefits of the integration of ontology alignment and debugging. We have enabled interactive comparative exploration and evaluation of multiple alignments at different levels of detail by developing a dedicated visual environment—Alignment Cubes—which allows for alignments’ evaluation even in the absence of reference alignments. Inspired by the latest technological advances we have investigated and identified three promising directions for the application of large, high-resolution displays in the field: improving the navigation in the ontologies and their alignments, supporting reasoning and collaboration between users.