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.

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This thesis is a linguistic/ontological inquiry into narrative dynamics. Particular attention is drawn to elucidating the mechanism for recognising story events as one reads narrative discourse. The overall discussion is a criticism of formal approaches to narrative dynamics which tend to make observations on the assumption that there is a fixed relation between language form and meaning (e.g. the distinction between events and non-events in narrative circumstances). As two possible factors responsible for preventing formal analysts from taking an elastic view of story-event structure in narrative, I point out overly metalinguistic and metatemporal attitudes held by many narrative poeiticians, grammarians and formal semanticists. The recognition of narrative dynamics is primarily concerned with our concept of time, so that this thesis focuses a good deal of attention on explicating how time can be conceptualised in narrative. The basic component of the argument, therefore, is made up of ontological observations concerning time, event, and change, which are mainly made in Chapters 3 and 5. This thesis concludes that overly metalinguistic and metatemporal approaches to narrative dynamics tend to be fallacious, and that it is the commonsensical view that counts in the recognition of the event structure in narrative discourse. A hypothetical stance I adopt in constructing a narrative theory is the viewpoint of the ordinary reader of narrative fiction who is not formally trained, and therefore, does not necessarily respond to narrative texts in a highly metalinguistic or metatemporal way. The importance of assuming the ordinary reader's viewpoint for the proper recognition of the story-event structure of narrative is referred to in many different respects throughout the thesis.

Data provenance refers to the lineage or pedigree of data, including information such as its origin and key events that affect it over the course of its lifecycle. In recent years, provenance has become increasingly important as more and more people are using data that they themselves did not generate. Tracking data provenance helps ensure that data provided by many different providers and sources can be trusted and used appropriately. Data provenance also has several other critical uses, including data quality assessment, generating data replication recipes, data security management, etc.One of the major objectives of our research is to investigate the semantics or meaning of data provenance. We describe a generic ontology of data provenance called the W7 model that represents the semantics of data provenance. Formalized in the conceptual graph formalism, the W7 model represents provenance as a combination of seven interconnected elements including "what," "when," "where," "how," "who," "which" and "why." The W7 model is designed to be general and comprehensive enough to cover a broad range of provenance-related vocabularies. However, the W7 model alone, no matter how comprehensive it is, is insufficient for capturing all domain-specific provenance requirements. We hence present a novel approach to developing domain ontologies of provenance. This approach relies on various conceptual graph mechanisms, including schema definitions and canonical formation rules, and enables us to easily adapt and extend the W7 model to develop domain ontologies of provenance. The W7 model for data provenance has been widely adopted and adapted for use within Raytheon Missile Systems and the iPlant Collaborative, as well as the US Army's ATRAP IV (Asymmetric Threat Response and Analysis Program) system.We also developed a domain ontology of provenance for Wikipedia based on the W7 model. This domain ontology enables us to extract provenance for each Wikipedia article. We present a study in which we use their provenance to assess the quality of Wikipedia articles. Assessing and guaranteeing data quality has become a critical concern that, to a large extent, determines the future success and survival of Wikipedia since the quality of Wikipedia has been continuously called into question due to various incidents of vandalism and misinformation since its launch in 2001. Our study shows that the quality of Wikipedia articles depends not only on the different types of contributors but also on how they collaborate. We identify a number of contributor roles based on the provenance. Based on the roles and provenance, our research identifies several collaboration patterns that are preferable or detrimental for data quality, thus providing insights for designing tools and mechanisms to improve Wikipedia article quality.

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This work is based upon fieldwork carried out among indigenous Pehuenche people living in the Andes in Southern Chile. It is an ethnographic investigation of the relations between Pehuenche vision and healing practices in different local settings. The first part of this thesis focuses on Pehuenche vision from a cosmo-political angle. In order to set the scene for my overall argument, I explore the constitutive relation between mutual vision among real people (Ch. che) and the emergence of the Pehuenche person, which I call the ‘dynamic personal composition.’ With mutual vision between people being a precondition for the emergence of social relations, I examine the experience of particular witchcraft actions in which mutual vision is not possible. This leads to the conceptualization of ‘unilateral vision’ as a key phenomenon associated with the emergence of illnesses and the alteration of the shared plane of Pehuenche visibility. I also explore how mutual vision can be restored only through the assemblage of particular visual capacities known in the vernacular as ‘the gift of vision.’ In the second part of the thesis, I analyze the ways in which public health services respond to particular illnesses not detectable or treatable by medical technicians. In particular, I focus on the implications of ‘the visualization of traditional healers,’ inherent in the State’s approach to intercultural health. Through the examination of both particular intercultural health projects, as well as local expressions of discontent and animosity towards the State, this thesis seeks to create awareness about the ontological relevance of mutual vision in relations among real people. By pointing out the equivocal understandings of the visible and the invisible domains within intercultural relations, the analysis as a whole seeks to explain why Pehuenche vision must be understood through ontological examination rather than through a multicultural approach.