Complex and chronic health conditions with multiple diagnoses and lacking in clinical practice guidelines often require a multidisciplinary care management scheme. Research has shown that the domain knowledge for these conditions is multidisciplinary, inconsistent, nonstandardized and poorly categorized making them heterogeneous and consequently challenging for collaborative work. The application of the boundary objects approach has come to the forefront as a way of closing communication gaps in collaborative work. There are limited research efforts in the application of boundary objects in the health care field and almost none in the area of complex chronic conditions. Research investigation of the application of boundary objects in heterogeneous domains is also limited. The primary objective(s) of this thesis is (are) to develop, test and evaluate a model and a methodology for creating boundary objects in the heterogeneous domain of complex chronic conditions. The methodology in this research applies a two-staged approach for enabling interoperability in the domain. The first stage is the development of a controlled vocabulary as a boundary object and the second stage of the two-staged approach is the development of an ontology as a boundary object to generate syntactic, semantic and pragmatic levels of interoperability in the dynamic domain. Towards these objectives, the boundary objects developed in the study satisfy certain unique requirements, namely to, have pragmatic boundaries, be dynamic in nature and be in standardized forms. To the best of our knowledge, this research is the first to investigate the development of boundary objects in the heterogeneous domain of complex chronic conditions. The outcome of this research is the development of a model for the generation of boundary objects to enhance communication among multidisciplinary clinicians. The model is developed in the heterogeneous domain of two complex chronic health conditions, namely, multiple chemical sensitivity and chronic pain. A testing and an evaluation process conducted in this research demonstrates that a high percentage of clinicians (>80%) agree on the overall usefulness of the boundary objects developed in this research. The results from the research are promising in terms of the potential applications of boundary objects in closing communication gaps in the multidisciplinary management of complex conditions.

Reasoning about processes in applications such as manufacturing, web services, enterprise modeling, and planning requires the representation of composite processes with complicated flows of control. Previous research in process representation has used formalisms such as Event Systems, Petri nets, and the Unified Modeling Language activity diagrams. The computational hardness of temporal projection problems in Event Systems has been extensively examined in the literature, whereas Petri nets and UML activity diagrams are applied to describe more elaborate processes. This thesis takes a systematic look into the temporal reasoning problems in Event Systems and assigns accurate semantics to both Petri nets and, for the first time, to UML activity diagrams. We give an analysis of computational complexity in temporal projection problems by exploring the boundary between their tractable and intractable subproblems. Our results provide new insights into the prominent role the properties of partial ordering play, however we also show that partial ordering is not the sole source of the intractability as has been claimed in an earlier work by Nebel and B{\"a}ckstr{\"o}m. Two influential modeling languages, Petri nets and UML activity diagrams, are axiomatized as two Basic Action Theories of Situation Calculus. They are called, respectively, SCOPE (Situation Calculus Ontology of PEtri nets) and SCAD (Situation Calculus theory of Activity Diagrams). We provide a Prolog implementation of SCOPE and prove the correctness of this program for regressable queries. We use SCAD to axiomatize the structural and dynamic properties of UML activity diagrams and also provide the first set of computational results with regard to the reachability problems in activity diagrams. The correctness of each of these two axiomatizations is also demonstrated by proving that the theory is satisfiable, and the intended interpretation corresponds to a model of the theory.

Reasoning about processes in applications such as manufacturing, web services, enterprise modeling, and planning requires the representation of composite processes with complicated flows of control. Previous research in process representation has used formalisms such as Event Systems, Petri nets, and the Unified Modeling Language activity diagrams. The computational hardness of temporal projection problems in Event Systems has been extensively examined in the literature, whereas Petri nets and UML activity diagrams are applied to describe more elaborate processes. This thesis takes a systematic look into the temporal reasoning problems in Event Systems and assigns accurate semantics to both Petri nets and, for the first time, to UML activity diagrams. We give an analysis of computational complexity in temporal projection problems by exploring the boundary between their tractable and intractable subproblems. Our results provide new insights into the prominent role the properties of partial ordering play, however we also show that partial ordering is not the sole source of the intractability as has been claimed in an earlier work by Nebel and B{\"a}ckstr{\"o}m. Two influential modeling languages, Petri nets and UML activity diagrams, are axiomatized as two Basic Action Theories of Situation Calculus. They are called, respectively, SCOPE (Situation Calculus Ontology of PEtri nets) and SCAD (Situation Calculus theory of Activity Diagrams). We provide a Prolog implementation of SCOPE and prove the correctness of this program for regressable queries. We use SCAD to axiomatize the structural and dynamic properties of UML activity diagrams and also provide the first set of computational results with regard to the reachability problems in activity diagrams. The correctness of each of these two axiomatizations is also demonstrated by proving that the theory is satisfiable, and the intended interpretation corresponds to a model of the theory.

Thèse (M.Sc.)--Université Laval, 2006. / Titre de l'écran-titre (visionné le 28 mars 2007). Bibliogr.

Τα φαινόμενα απάτης τείνουν να κυριαρχήσουν τις τελευταίες δεκαετίες σε κάθε τομέα. Ένας τομέας που πλήττεται ιδιαίτερα στις μέρες μας είναι αυτός της υγειονομικής περίθαλψης γενικά και ειδικά της συνταγογράφησης των φαρμάκων. Οι υγειονομικές υπηρεσίες είναι ιδιαίτερα τρωτές στην απάτη και την κατάχρηση. Τόσο οι φορείς κοινωνικής ασφάλισης, όσο και οι ιδιωτικές ασφαλιστικές εταιρείες χάνουν όλο και περισσότερα χρήματα κάθε χρόνο, λόγω ψευδών αιτιών αποζημιώσεων. Το αντικείμενο της παρούσας διατριβής είναι ο σχεδιασμός και η ανάπτυξη μιας μεθοδολογίας ανίχνευσης και πρόληψης της απάτης, που θα μπορεί να εφαρμοστεί στις επιχειρησιακές διεργασίες των υπηρεσιών υγειονομικής περίθαλψης και θα εξασφαλίζει την ελαχιστοποίηση της απώλειας των σχετικών κεφαλαίων. Η ίδια θα είναι σε θέση να ανιχνεύει τα ύποπτα προς απάτη περιστατικά, εξασφαλίζοντας έτσι την ποιότητα και την συνέπεια των παρεχόμενων υπηρεσιών. / Fraud phenomena tend to dominate the last decades. A sector that is particularly affected in our days is that of healthcare domain in general and specifically prescriptions reimbursement. Healthcare services are particularly vulnerable in fraud and abuse. Not only institutions of social insurance, but also private companies lose more money each year, because of false causes of compensations. This thesis intends to illustrate the planning and development of a fraud detection methodology, which is accompanied and supported by a generic fraud ontological framework. This methodology will be able to detect erroneous or suspicious records, ensuring thus the quality and the consequence of provided services.

Στην παρούσα εργασία αναφερόμαστε στις δυνατότητες αξιοποίησης των Οντολογιών στην Εκπαίδευση. Το αντικείμενο είναι ο σχεδιασμός συστήματος Εκπαίδευσης στη Στατιστική ,το οποίο θα χρησιμοποιεί οντολογίες για την αναπαράσταση του γνωστικού αντικειμένου και του εκπαιδευτικού περιεχομένου. Η ανάπτυξη των οντολογιών θα γίνει με το περιβάλλον Protégé. Στο πρώτο κεφάλαιο θα κάνουμε μια επισκόπηση στην έννοια της Οντολογίας. Θα αναφερθούμε στον ορισμό και στις δυνατότητες της, στα είδη των οντολογιών, στην κατηγοριοποιησή τους και στις γλώσσες αναπαράστασης οντολογιών. Θα γίνει μια συνοπτική παρουσίαση των εργαλείων και των μεθοδολογιών ανάπτυξης των οντολογιών. Στο δεύτερο κεφάλαιο αναλύεται η χρήση των οντολογιών στην Εκπαίδευση και συγκεκριμένα οι μαθησιακές οντολογιές που μπορούν να χρησιμοποιηθούν για την ανάπτυξη ευφυών εκπαιδευτικών πληροφοριακών συστημάτων. Ο χρήστης μαθησιακού υλικού μπορεί να αναζητήσει μαθησιακό υλικό με το περιεχόμενο, τη μορφή και τη δομή του. Για τα συστήματα ηλεκτρονικής μάθησης οι διάφορες πτυχές των τμημάτων του μαθησιακού υλικού περιγράφονται απο τα μεταδεδομένα. Στο τρίτο κεφάλαιο θα δούμε τον ορισμό των μαθησιακών στόχων, ποιοί είναι οι μαθησιακοί στόχοι στην εκπαίδευση, ποιοί είναι οι διδακτικοί στόχοι και ποιά είναι τα σημαντικά τους στοιχεία. Στο τέλος του κεφαλαίου αυτού θα παρουσιαστεί η ταξινομιά Bloom, η οργάνωση και η κατηγοριοποίηση των δεξιοτήτων της σκέψης και των στόχων . Στο τέταρτο κεφάλαιο θα αναλύσουμε το πρότυπο μεταδεδομένων Scorm, το οποίο αποτελεί σήμερα τη σημαντικότερη πρωτοβουλία που αναπτύσσεται στον τομέα των προτύπων του e-Learning. Στο πέμπτο κεφάλαιο θα αναλύσουμε την έννοια της Στατιστικής που θα αποτελέσει το γνωστικό μας αντικείμενο για την δημιουργία της συνδυαστικής οντολογίας μας. Στο έκτο κεφάλαιο θα παρουσιάσουμε την μελέτη που πραγματοποιήθηκε στις θεματικές ενότητες της Πληροφορικής του Ελληνικού Ανοικτού Πανεπιστημίου. Στο έβδομο κεφάλαιο θα περιγράψουμε τον τρόπο κατασκευής των οντολογιών μας, Για την κάθε οντολογία που θα κατασκευάσουμε θα παρουσιαστεί ο λόγος ανάπτυξης της και το πεδίο ενδιαφέροντος, θα καθοριστούν οι ερωτήσεις επάρκειας για την κάθε οντολογία, θα γίνει λεπτομερής περιγραφή των κλάσεων, των ιδιοτήτων των κλάσεων και των στιγμιότυπων της κάθε οντολογίας, θα περιγραφεί λεπτομερός το περιβάλλον ανάπτυξης, η γλώσσα αναπαράστασης των οντολογιών και στο τέλος θα γίνει τεχνική και ποιοτική αξιολόγηση της οντολογίας. Η δοκιμή των Οντολογιών μας στο περιβάλλον Protégé έδειξε πως το μοντέλο διαχείρισης μαθησιακών αντικειμένων και μαθησιακών στόχων που δημιουργήσαμε λειτουργεί αποτελεσματικά σε σχέση με τους στόχους που είχαμε θέσει αφου μας δίνει τη δυνατότητα να ορίσουμε με τυπικό τρόπο βασικές συνιστώσες της μαθησιακής διαδικασίας. / -

Thanks to the affordability of DNA sequencing, hundreds of thousands of individuals with rare disorders are undergoing whole-genome sequencing in an effort to reveal novel disease aetiologies, increase our understanding of biological processes and improve patient care. However, the power to discover the genetic causes of many unexplained rare diseases is hindered by a paucity of cases with a shared molecular aetiology. This thesis presents research into statistical and computational methods for determining the genetic causes of rare diseases. Methods described herein treat important aspects of the nature of rare diseases, including genetic and phenotypic heterogeneity, phenotypes involving multiple organ systems, Mendelian modes of inheritance and the incorporation of complex prior information such as model organism phenotypes and evolutionary conservation. The complex nature of rare disease phenotypes and the need to aggregate patient data across many centres has led to the adoption of the Human Phenotype Ontology (HPO) as a means of coding patient phenotypes. The HPO provides a standardised vocabulary and captures relationships between disease features. I developed a suite of software packages dubbed 'ontologyX' in order to simplify analysis and visualisation of such ontologically encoded data, and enable them to be incorporated into complex analysis methods. An important aspect of the analysis of ontological data is quantifying the semantic similarity between ontologically annotated entities, which is implemented in the ontologyX software. We employed this functionality in a phenotypic similarity regression framework, 'SimReg', which models the relationship between ontologically encoded patient phenotypes of individuals and rare variation in a given genomic locus. It does so by evaluating support for a model under which the probability that a person carries rare alleles in a locus depends on the similarity between the person's ontologically encoded phenotype and a latent characteristic phenotype which can be inferred from data. A probability of association is computed by comparison of the two models, allowing prioritisation of candidate loci for involvement in disease with respect to a heterogeneous collection of disease phenotypes. SimReg includes a sophisticated treatment of HPO-coded phenotypic data but dichotomises the genetic data at a locus. Therefore, we developed an additional method, 'BeviMed', standing for Bayesian Evaluation of Variant Involvement in Mendelian Disease, which evaluates the evidence of association between allele configurations across rare variants within a genomic locus and a case/control label. It is capable of inferring the probability of association, and conditional on association, the probability of each mode of inheritance and probability of involvement of each variant. Inference is performed through a Bayesian comparison of multiple models: under a baseline model disease risk is independent of allele configuration at the given rare variant sites and under an alternate model disease risk depends on the configuration of alleles, a latent partition of variants into pathogenic and non-pathogenic groups and a mode of inheritance. The method can be used to analyse a dataset comprising thousands of individuals genotyped at hundreds of rare variant sites in a fraction of a second, making it much faster than competing methods and facilitating genome-wide application.

Assessment is a well understood educational topic with a really long history and a wealth of literature. Given this level of understanding of the topic, educational practitioners are able to differentiate, for example, between valid and invalid assessments. Despite the fact that we can test for the validity of an assessment, knowing how to systematically generate a valid assessment is still challenging and needs to be understood. In this thesis we introduce a similarity-based method to generate a specific type of questions, namely multiple choice questions, and control their difficulty. This form of questions is widely used especially in contexts where automatic grading is a necessity. The generation of MCQs is more challenging than generating open-ended questions due to the fact that their construction includes the generation of a set of answers. These answers need to be all plausible, otherwise the validity of the question can be questionable. Our proposed generation method is applicable to both manual and automatic gener- ation. We show how to implement it by utilising ontologies for which we also develop similarity measures. Those measures are simply functions which compute the similarity, i.e., degree of resemblance, between two concepts based on how they are described in a given ontology. We show that it is possible to control the difficulty of an MCQ by varying the degree of similarity between its answers. The thesis and its contributions can be summarised in a few points. Firstly, we provide literature reviews for the two main pillars of the thesis, namely question generation and similarity measures. Secondly, we propose a method to automatically generate MCQs from ontologies and control their difficulty. Thirdly, we introduce a new family of similarity measures. Fourthly, we provide a protocol to evaluate a set of automatically generated assessment questions. The evaluation takes into account experts' reviews and students' performance. Finally, we introduce an automatic approach which makes it possible to evaluate a large number of assessment questions by simulating a student trying to answer the questions.

Module extraction is an important reasoning task, aiding in the design, reuse and maintenance of ontologies. Reasoning services such as subsumption testing and MinA extraction have been shown to bene t from module extraction methods. Though various syntactic traversal-based module extraction algorithms exist for extracting modules, many only consider the subsumee of a subsumption statement as a selection criterion for reducing the axioms in the module. In this dissertation we extend the bottom-up reachability-based module extraction heuristic for the inexpressive Description Logic EL, by introducing a top-down version of the heuristic which utilises the subsumer of a subsumption statement as a selection criterion to minimize the number of axioms in a module. Then a combined bidirectional heuristic is introduced which uses both operands of a subsumption statement in order to extract very small modules. We then investigate the relationship between MinA extraction and bidirectional reachabilitybased module extraction. We provide empirical evidence that bidirectional reachability-based module extraction for subsumption entailments in EL provides a signi cant reduction in the size of modules for almost no additional costs in the running time of the original algorithms. / Computer Science / M. Sc. (Computer Science)

Com o advento da Internet, novas tecnologias de Geoprocessamento têm sido criadas para tratar, trocar, disponibilizar e acessar informações e dados espaciais como as Infraestruturas de Dados Espaciais, os Geobrowsers e os Serviços de Informações Geográficas. O número de aplicações que lida com atributos espaciais não somente cresceu como também se diversificou, no entanto problemas de interoperabilidade semântica ainda limitam a evolução nessa área. Ontologias formalizam o conhecimento necessário para organizar e permitir o uso de dados de diferentes fontes, pois são modelos de referência robustos devido à sua expressividade e capacidade de serem compartilhados pela internet. Nesta tese, ontologias foram desenvolvidas para aumentar a interoperabilidade semântica em sistemas de apoio à logística humanitária que utilizam serviços de informações geográficas. A aplicação de logística humanitária estudada foi a operação de bancos de alimentos. O conhecimento relativo aos processos logísticos, problemas logísticos de bancos de alimentos e serviços de informações geográficas úteis para os métodos de solução desses problemas foram formalizados em uma rede de ontologias. O número de serviços de informações geográficas disponíveis ainda é pequeno, mas a composição de serviços de informações geográficas em cadeias, formando novos serviços, abre uma perspectiva para que operações espaciais, não fiquem mais restritas às soluções proprietárias e possam ser melhor exploradas. As ontologias propostas neste trabalho podem ser usadas como base para o desenvolvimento de sistemas em que serviços de informações geográficas podem ser acoplados, na medida em que forem sendo disponibilizados. / With the advent of Internet, new technologies from GIS field have been created to access and exchange spatial data and information, such as Spatial Data Infrastructures, Geobrowsers and Geographic Information Services. The number of applications dealing with spatial attributes is growing and is also diversifying. However semantic interoperability problems still limit progress in this area. Ontologies formalize the knowledge necessary to organize and allow the use of data from different sources due to its expressiveness and ability to be shared over the Internet. In this thesis, ontologies have been developed to increase the semantic interoperability of humanitarian logistics support systems that use geographic information services. The application of humanitarian logistics operation studied was the food banks operation. The knowledge on logistics processes, logistics problems of food banks and geographic information services useful for the methods for solving these problems have been formalized into a network of ontologies. The number of geographical information services available is still small, but the composition of geographic information services in chains, creating new services, opens a perspective for new methods of spatial operations, which are not limited to proprietary solutions form GIS softwares available in the market. The ontologies proposed in this thesis can be used as a basis for developing systems in which geographic information services can be coupled, as it becomes available.