Ontologies play key roles in many applications today. Therefore, whether using a newly-specified ontology or an existing ontology for use in its target application, it is important to determine the suitability of an ontology to the application at hand. This need is addressed by carrying out ontology evaluation, which determines qualities of an ontology using methodologies, criteria or measures. However, for addressing the ontology requirements from a given application, it is necessary to determine what the appropriate set of criteria and measures are. In this thesis, we propose a Requirements-Oriented Methodology for Evaluating Ontologies (ROMEO). ROMEO outlines a methodology for determining appropriate methods for ontology evaluation that incorporates a suite of existing ontology evaluation criteria and measures. ROMEO helps ontology engineers to determine relevant ontology evaluation measures for a given set of ontology requirements by linking these requirements to existing ontology evaluation measures through a set of questions. There are three main parts to ROMEO. First, ontology requirements are elicited from a given application and form the basis for an appropriate evaluation of ontologies. Second, appropriate questions are mapped to each ontology requirement. Third, relevant ontology evaluation measures are mapped to each of those questions. From the ontology requirements of an application, ROMEO is used to determine appropriate methods for ontology evaluation by mapping applicable questions to the requirements and mapping those questions to appropriate measures. In this thesis, we perform the ROMEO methodology to obtain appropriate ontology evaluation methods for ontology-driven applications through case studies of Lonely Planet and Wikipedia. Since the mappings determined by ROMEO are dependent on the analysis of the ontology engineer, the validation of these mappings is needed. As such, in addition to proposing the ROMEO methodology, a method for the empirical validation of ROMEO mappings is proposed in this thesis. We report on two empirical validation experiments that are carried out in controlled environments to examine the performance of the ontologies over a set of tasks. These tasks vary and are used to compare the performance of a set of ontologies in the respective experimental environment. The ontologies used vary on a specific ontology quality or measure being examined. Empirical validation experiments are conducted for two mappings between questions and their associated measures, which are drawn from case studies of Lonely Planet and Wikipedia. These validation experiments focus on mappings between questions and their measures. Furthermore, as these mappings are application-independent, they may be reusable in subsequent applications of the ROMEO methodology. Using a ROMEO mapping from the Lonely Planet case study, we validate a mapping of a coverage question to the F-measure. The validation experiment carried out for this mapping was inconclusive, thus requiring further analysis. Using a ROMEO mapping from the Wikipedia case study, we carry out a separate validation experiment examining a mapping between an intersectedness question and the tangledness measure. The results from this experiment showed the mapping to be valid. For future work, we propose additional validation experiments for mappings that have been identified between questions and measures.

In biomedical research, ontologies are widely used to represent knowledge as well as to annotate datasets. Many of the existing ontologies cover a single type of phenomena, such as a process, cell type, gene, pathological entity or anatomical structure. Consequently, there is a requirement to use multiple ontologies to fully characterize the observations in the datasets. Although this allows precise annotation of different aspects of a given dataset, it limits our ability to use the ontologies in data analysis, as the ontologies are usually disconnected and their combinations cannot be exploited. Motivated by this, here we present novel ontology design methods for combining pathology and anatomy concepts. To this end, we use a dataset of mouse models which has been characterized through two ontologies: one of them is the mouse pathology ontology (MPATH) covering pathological lesions while the other is the mouse anatomy ontology (MA) covering the anatomical site of the lesions. We propose four novel ontology design patterns for combining these ontologies, and use these patterns to generate four ontologies in a data-driven way. To evaluate the generated ontologies, we utilize these in ontology-based data analysis, including ontology enrichment analysis and computation of semantic similarity. We demonstrate that there are significant differences between the four ontologies in different analysis approaches. In addition, when using semantic similarity to confirm the hypothesis that genetically identical mice should develop more similar diseases, the generated combined ontologies lead to significantly better analysis results compared to using each ontology individually. Our results reveal that using ontology design patterns to combine different facets characterizing a dataset can improve established analysis methods.

With the emerging amount of information available in the internet, how to make full use of this information becomes an urgent issue. One of the solutions is using ontology alignment to aggregate different sources of information in order to get comprehensive and complete information. Scalability is a problem regarding the ontology alignment and it can be settled down by reducing the search space of mapping suggestions. In this paper we propose an automated procedure mainly using different clustering techniques to prune the search space. The main focus of this paper is to evaluate different clustering related techniques to be applied in our system. K-means, Chameleon and Birch have been studied and evaluated, every parameter in these clustering algorithms is studied by doing experiments separately, in order to find the best clustering setting to the ontology clustering problem. Four different similarity assignment methods are researched and analyzed as well. Tfidf vectors and cosine similarity are used to identify the similar clusters in the two ontologies, experiments about threshold of cosine similarity are made to get the most suitable value. Our system successfully builds an automated procedure to generate reduced search space for ontology alignment, on one hand, the result shows that it reduces twenty to ninety times of comparisons that the ontology alignment was supposed to make, the precision goes up as well. On the other hand, it only needs one to two minutes of execution time, meanwhile the recall and f-score only drop down a little bit. The trade- off is acceptable for the ontology alignment system which will take tens of minutes to generate the ontology alignment of the same ontology set. As a result, the large scale ontology alignment becomes more computable and feasible.

Ontologies are widely used in various domains, including biomedical research, to structure information, represent knowledge, and analyze data. The combination of ontologies from different domains is crucial for systematic data analysis and comparison of similar domains. This process requires ontology composition, integration, and alignment, which involve creating new classes by reusing classes from different domains, aggregating types of ontologies within the same domain, and finding correspondences between ontologies within the same or similar domain. This thesis presents use cases where we applied ontology composition, integration, and alignment of phenotype ontologies, and evaluated the resulting ontologies and alignment. First, we analyzed a large aging dataset of inbred laboratory mice, using Mouse Anatomy and Mouse Pathology ontologies. Second, we integrated phenotype ontologies for human and model organism phenotypes to enable comparisons of phenotypes between and within individual species. We developed Pheno-e, an extension of PhenomeNet. We identified novel abnormal anatomical classes for fly phenotypes, allowing the annotation of fly genes that were not annotated before. We demonstrate the distinct contributions of each species' phenotypic data to detecting human diseases using Pheno-e, and show that mouse phenotypic data contributes the most to the discovery of gene--disease associations. This work could guide the selection of model organisms when building methods to find gene-disease associations. Additionally, we refined class definitions in phenotypic ontologies, specifically targeting cell cardinality phenotypes. This representation resolved incorrect inferences in the utilized ontologies, enabling accurate interpretation of phenotypic descriptions. Our findings reveal that this correction enhances gene-disease prediction for diseases associated with cardinality phenotypes. Third, we introduce a novel neural-symbolic method that combines logic fundamentals with machine learning for ontology alignment. This method begins with symbolic representation, followed by iterative neural learning for alignment and symbolic representation consistency checking and reasoning, and back to neural learning. We demonstrate that our system generates noncontroversial alignments first and these alignments are coherent with respect to OWL EL. This novel method can pave the way for more accurate and efficient ontology-based methods, which can have significant implications for various semantic web applications.

The study of human affective states and their influences has been a research interest in psychology for some time. Fortunately, the presence of an affective computing paradigm allows us to use theories and findings from the discipline of psychology in the representation and development of human affective applications. However, because of the complexity of the subject, it is possible to misunderstand concepts that are shared via human and/or computer communications. With the appearance of technological innovations in our lives, for instance the SemanticWeb and the Web Ontology Language (OWL), there is a stronger need for computers to better understand human affective states and their influences. The use of an ontology can be beneficial in order to represent human affective states and their influences in a machine-understandable format. Truly, ontologies provide powerful tools to make sense of data. Our thesis proposes HASIO, a Human Affective States and their Influences Ontology, designed based on existing psychological theories. HASIO was developed to represent the knowledge that is necessary to model affective states and their influences in a computerized format. It describes the human affective states (Emotion, Mood and Sentiment) and their influences (Personality, Need and Subjective well-being) and conceptualizes their models and recognition methods. HASIO also represents the relationships between affective states and the factors that influence them. We surveyed and analyzed existing ontologies regarding human affective states and their influences to realize the significance and profit of developing our proposed ontology (HASIO). We follow the Methontology approach, a comprehensive engineering methodology for ontology building, to design and build HASIO. An important aspect in determining the ontology scope is Competency Questions (CQs). We configure HASIO CQs by analyzing the resources from psychology theories, available lexicons and existing ontologies. In this thesis, we present the development, modularization and evaluation of HASIO. HASIO can profit from the modularization process by dividing the whole ontology in self-contained modules that are easy to reuse and maintain. The ontology is evaluated through Question Answering system (HASIOQA), a task-based evaluation system, for validation. We design and develop a natural language interface system for this purpose. Moreover, the proposed ontology was evaluated through the Ontology Pitfall Scanner for verification and correctness against several criteria. Furthermore, HASIO was used in sentiment analysis on diffrent Twitter dataset. We designed and developed a tweet polarity calculation algorithm. Additionally, we compare our ontology result with machine learning technique. We demonstrate and highlight the advantage of using ontology in sentiment analysis.

Na atualidade, o interesse pelo uso de ontologias tem sido incrementado. No entanto, o processo de construção pode ser custoso em termos de tempo. Para uma ontologia ser construída, precisa-se de um especialista com conhecimentos de um editor de ontologias. Com a finalidade de reduzir tal processo de construção pelo especialista, analisamos e propomos um método para realizar aprendizado de ontologias (AO) de forma supervisionada. O presente trabalho consiste em uma abordagem combinada de diferentes técnicas no AO. Primeiro, usamos uma técnica estatística chamada C/NC-values, acompanhada da ferramenta Cogroo, para extrair os termos mais representativos do texto. Esses termos são considerados por sua vez como conceitos. Projetamos também uma gramática de restrições (GR), com base na informação linguística do Português, com o objetivo de reconhecer e estabelecer relações entre conceitos. Para poder enriquecer a informação na ontologia, usamos a análise de conceitos formais (ACF) com o objetivo de identificar possíveis superconceitos entre dois conceitos. Finalmente, extraímos ontologias para os textos de três temas, submetendo-as à avaliação dos especialistas na área. Um web site foi feito para tornar o processo de avaliação mais amigável para os avaliadores e usamos o questionário de marcos de características proposto pelo método OntoMetrics. Os resultados mostram que nosso método provê um ponto de partida aceitável para a construção de ontologias. / Nowadays, the interest in the use of ontologies has increased, nevertheless, the process of ontology construction can be very time consuming. To build an ontology, we need a domain expert with knowledge in an ontology editor. In order to reduce the time needed by the expert, we propose and analyse a supervised ontology learning (OL) method. The present work consists of a combined approach of different techniques in OL. First, we use a statistic technique called C/NC-values, with the help of the Cogroo tool, to extract the most significant terms. These terms are considered as concepts consequently. We also design a constraint grammar (CG) based in linguistic information of Portuguese to recognize relations between concepts. To enrich the ontology information, we use the formal concept analysis (FCA) in order to discover a parent for a set of concepts. In order to evaluate the method, we have extracted ontologies from text on three different domains and tested them with corresponding experts. A web site was built to make the evaluation process friendlier for the experts and we used an evaluation framework proposed in the OntoMetrics method. The results show that our method provides an acceptable starting point for the construction of ontologies.

Na atualidade, o interesse pelo uso de ontologias tem sido incrementado. No entanto, o processo de construção pode ser custoso em termos de tempo. Para uma ontologia ser construída, precisa-se de um especialista com conhecimentos de um editor de ontologias. Com a finalidade de reduzir tal processo de construção pelo especialista, analisamos e propomos um método para realizar aprendizado de ontologias (AO) de forma supervisionada. O presente trabalho consiste em uma abordagem combinada de diferentes técnicas no AO. Primeiro, usamos uma técnica estatística chamada C/NC-values, acompanhada da ferramenta Cogroo, para extrair os termos mais representativos do texto. Esses termos são considerados por sua vez como conceitos. Projetamos também uma gramática de restrições (GR), com base na informação linguística do Português, com o objetivo de reconhecer e estabelecer relações entre conceitos. Para poder enriquecer a informação na ontologia, usamos a análise de conceitos formais (ACF) com o objetivo de identificar possíveis superconceitos entre dois conceitos. Finalmente, extraímos ontologias para os textos de três temas, submetendo-as à avaliação dos especialistas na área. Um web site foi feito para tornar o processo de avaliação mais amigável para os avaliadores e usamos o questionário de marcos de características proposto pelo método OntoMetrics. Os resultados mostram que nosso método provê um ponto de partida aceitável para a construção de ontologias. / Nowadays, the interest in the use of ontologies has increased, nevertheless, the process of ontology construction can be very time consuming. To build an ontology, we need a domain expert with knowledge in an ontology editor. In order to reduce the time needed by the expert, we propose and analyse a supervised ontology learning (OL) method. The present work consists of a combined approach of different techniques in OL. First, we use a statistic technique called C/NC-values, with the help of the Cogroo tool, to extract the most significant terms. These terms are considered as concepts consequently. We also design a constraint grammar (CG) based in linguistic information of Portuguese to recognize relations between concepts. To enrich the ontology information, we use the formal concept analysis (FCA) in order to discover a parent for a set of concepts. In order to evaluate the method, we have extracted ontologies from text on three different domains and tested them with corresponding experts. A web site was built to make the evaluation process friendlier for the experts and we used an evaluation framework proposed in the OntoMetrics method. The results show that our method provides an acceptable starting point for the construction of ontologies.

This thesis would not be made possible without the generous support of IATA. / Les taxonomies sont une représentation essentielle des connaissances, jouant un rôle central dans de nombreuses applications riches en connaissances. Malgré cela, leur construction est laborieuse que ce soit manuellement ou automatiquement, et l'évaluation quantitative de taxonomies est un sujet négligé. Lorsque les chercheurs se concentrent sur la construction d'une taxonomie à partir de grands corpus non structurés, l'évaluation est faite souvent manuellement, ce qui implique des biais et se traduit souvent par une reproductibilité limitée. Les entreprises qui souhaitent améliorer leur taxonomie manquent souvent d'étalon ou de référence, une sorte de taxonomie bien optimisée pouvant service de référence. Par conséquent, des connaissances et des efforts spécialisés sont nécessaires pour évaluer une taxonomie. Dans ce travail, nous soutenons que l'évaluation d'une taxonomie effectuée automatiquement et de manière reproductible est aussi importante que la génération automatique de telles taxonomies. Nous proposons deux nouvelles méthodes d'évaluation qui produisent des scores moins biaisés: un modèle de classification de la taxonomie extraite d'un corpus étiqueté, et un modèle de langue non supervisé qui sert de source de connaissances pour évaluer les relations hyperonymiques. Nous constatons que nos substituts d'évaluation corrèlent avec les jugements humains et que les modèles de langue pourraient imiter les experts humains dans les tâches riches en connaissances. / Taxonomies are an essential knowledge representation and play an important role in classification and numerous knowledge-rich applications, yet quantitative taxonomy evaluation remains to be overlooked and left much to be desired. While studies focus on automatic taxonomy construction (ATC) for extracting meaningful structures and semantics from large corpora, their evaluation is usually manual and subject to bias and low reproducibility. Companies wishing to improve their domain-focused taxonomies also suffer from lacking ground-truths. In fact, manual taxonomy evaluation requires substantial labour and expert knowledge. As a result, we argue in this thesis that automatic taxonomy evaluation (ATE) is just as important as taxonomy construction. We propose two novel taxonomy evaluation methods for automatic taxonomy scoring, leveraging supervised classification for labelled corpora and unsupervised language modelling as a knowledge source for unlabelled data. We show that our evaluation proxies can exert similar effects and correlate well with human judgments and that language models can imitate human experts on knowledge-rich tasks.