An ontologically founded architecture for information systems in clinical and epidemiological research

This paper presents an ontologically founded basic architecture for information systems, which are intended to capture, represent, and maintain metadata for various domains of clinical and epidemiological research. Clinical trials exhibit an important basis for clinical research, and the accurate specification of metadata and their documentation and application in clinical and epidemiological study projects represents a significant expense in the project preparation and has a relevant impact on the value and quality of these studies

OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research

Background: The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct representation of their metadata. In various research organizations, which are planning and coordinating studies, the required metadata are specified differently, depending on many conditions, e.g., on the used study management software. The latter does not always meet the needs of a particular research organization, e.g., with respect to the relevant metadata attributes and structuring possibilities. Methods: The objective of the research, set forth in this paper, is the development of a new approach for ontology-based representation and management of metadata. The basic features of this approach are demonstrated by the software tool OntoStudyEdit (OSE). The OSE is designed and developed according to the three ontology method. This method for developing software is based on the interactions of three different kinds of ontologies: a task ontology, a domain ontology and a top-level ontology. Results: The OSE can be easily adapted to different requirements, and it supports an ontologically founded representation and efficient management of metadata. The metadata specifications can by imported from various sources; they can be edited with the OSE, and they can be exported in/to several formats, which are used, e.g., by different study management software. Conclusions: Advantages of this approach are the adaptability of the OSE by integrating suitable domain ontologies, the ontological specification of mappings between the import/export formats and the DO, the specification of the study metadata in a uniform manner and its reuse in different research projects, and an intuitive data entry for non-expert users

Towards an Ontology-Based Phenotypic Query Model

Clinical research based on data from patient or study data management systems plays an important role in transferring basic findings into the daily practices of physicians. To support study recruitment, diagnostic processes, and risk factor evaluation, search queries for such management systems can be used. Typically, the query syntax as well as the underlying data structure vary greatly between different data management systems. This makes it difficult for domain experts (e.g., clinicians) to build and execute search queries. In this work, the Core Ontology of Phenotypes is used as a general model for phenotypic knowledge. This knowledge is required to create search queries that determine and classify individuals (e.g., patients or study participants) whose morphology, function, behaviour, or biochemical and physiological properties meet specific phenotype classes. A specific model describing a set of particular phenotype classes is called a Phenotype Specification Ontology. Such an ontology can be automatically converted to search queries on data management systems. The methods described have already been used successfully in several projects. Using ontologies to model phenotypic knowledge on patient or study data management systems is a viable approach. It allows clinicians to model from a domain perspective without knowing the actual data structure or query language

An ontology-based system to generate epidemiologic profiles

Epidemiology is a field of study in Medicine which seeks to understand the factors that determine the frequency and distribution of diseases in humans. This field allows one to understand the phenomena of health and disease of a particular population by generating this populations epidemiological profile. The knowledge provided in this profile allows a shift in the focus from treating to preventing diseases, which is an important aim of the current Brazilian health care program. This dissertation proposes a system to study the epidemiological profile in a basic health care unit. This system applies an ontology as basis for modeling and querying the epidemiological information. An ontology is a conceptual model which captures an specific view of a domain of discourse. This model may be used to structure the systems information, which later can be queried also with basis on this same ontology. A preliminary validation of this systems prototype has shown that it is able to successfully generate the health care units epidemiological profile, providing new knowledge about the patients and treatments involved in this unit. Such prototype may now be applied in this real setting to guide the actions of health care professionals in dealing with hypertension and other health conditions. In order to develop the system, a goal-oriented methodology based on Tropos is applied. This methodology guides software development since an early stage of organizational modeling until the systems implementation by using current standards for ontology implementation. Many of the available ontology engineering methodologies presuppose the existence of a set of questions which provide the objective and scope of the ontology under development. However, these so-called competency questions are not always clear from start. The highlight of the proposed methodology is applying goal analysis to assist the ontology engineer to reason about and model competency questions. Following this view, such competency questions are comparable to system requirements, elicited and modeled during the requirements engineering stage of a software development process. Both the developed system and the proposed methodology are contributions of this work. However, while the former has proven to be useful in practice, further steps must be carried out in order to properly validate the latter, by applying it to other cases

Eye tracking sentences in language education

The present study reports and discusses the use of eye tracking qualitative data (static and dynamic gaze plots and heatmaps) in reading workshops in a middle school and in Generative Syntax and Sentence Processing courses at the undergraduate and graduate levels. Both endeavors take the sentential level as the proper object to be metacognitively explored in language education in order to develop innate science forming capacity and knowledge of language. In both projects non-discrepant qualitative eye tracking data collected and quantitatively analyzed in psycholinguistic studies carried out in LAPEX-UFRJ (Experimental Psycholinguistics Laboratory of the Federal University of Rio de Janeiro) were displayed to students as a point of departure, triggering discussions. Active, problem-solving based methodologies were employed with the objective of stimulating student participation. The article also discusses the importance of developing full literacy, epistemic vigilance and intellectual self-defense in an infodemic world.The present study reports and discusses the use of eye tracking qualitative data (static and dynamic gaze plots and heatmaps) in reading workshops in a middle school and in Generative Syntax and Sentence Processing courses at the undergraduate and graduate levels. Both endeavors take the sentential level as the proper object to be metacognitively explored in language education in order to develop innate science forming capacity and knowledge of language. In both projects non-discrepant qualitative eye tracking data collected and quantitatively analyzed in psycholinguistic studies carried out in LAPEX-UFRJ (Experimental Psycholinguistics Laboratory of the Federal University of Rio de Janeiro) were displayed to students as a point of departure, triggering discussions. Active, problem-solving based methodologies were employed with the objective of stimulating student participation. The article also discusses the importance of developing full literacy, epistemic vigilance and intellectual self-defense in an infodemic world

Rethinking Causality, Complexity and Evidence for the Unique Patient

This open access book is a unique resource for health professionals who are interested in understanding the philosophical foundations of their daily practice. It provides tools for untangling the motivations and rationality behind the way medicine and healthcare is studied, evaluated and practiced. In particular, it illustrates the impact that thinking about causation, complexity and evidence has on the clinical encounter. The book shows how medicine is grounded in philosophical assumptions that could at least be challenged. By engaging with ideas that have shaped the medical profession, clinicians are empowered to actively take part in setting the premises for their own practice and knowledge development. Written in an engaging and accessible style, with contributions from experienced clinicians, this book presents a new philosophical framework that takes causal complexity, individual variation and medical uniqueness as default expectations for health and illness

Relationality and health: developing a transversal neurotheological account of the pathways linking social connection, immune function, and health outcomes

This thesis is a transdisciplinary investigation of the link between social connection and health outcomes. Its twofold aim is to explore the nature of this relationship and build a theoretical model for a possible causal chain between the two, and to develop and deploy a new model for engaging the very different discourses of theology and neuroscience. To this end it draws on both theological reflection and on experimental scientific data from cognitive neuroscience and psychoneuroimmunology. The opening half of the work establishes the wider epistemological and methodological frameworks within which the project is set, and also the specific framework for the particular area of study. The first of these involves a critical analysis of the tensions at the heart of the dialogue between science and religion, and of the specific difficulties faced by the emerging sub-discipline of neurotheology. It then dissects and further develops the interdisciplinary dialogical model devised by J Wentzel van Huyssteen, in order to enable it to generate and support additional transdisciplinary outputs. In the second of the two framework arenas, the concept of health itself is first explored, and then epidemiological, Biblical, and immunological accounts of the link between relational connection and health are examined in order to establish that sufficient common ground exists to warrant a neurotheological approach to investigating the question of how the two are connected. The second half of the thesis then uses the developed model as a basis for engaging theological and neuroscientific perspectives on human relationality. This takes the form of three transversal encounters, each centred around a specific aspect of this: relationality as basic, as emergent, and as realised. From the output of these three dialogical interactions, a neurotheologically framed argument is developed to support the contention that relationality is an emergent phenomenon of a complex system concerned with social monitoring and response, and thus the way in which it is realised can exert causal constraints on system components. Finally a theoretical model is derived from this argument for a pathway linking relational experience to health outcomes via alterations in allostatic maintenance mechanisms