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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Ontology design patterns are used for creating quality modeling solutions for ontologies. The presentation of ontology design patterns is concerned with reusability of ontologies from a user perspective. The purpose of this research is to identify improvement areas in the presentation of content ontology design patterns. The objective is to analyze different content ontology design patterns and provide suggestions for possible changes in current templates and pattern presentation. The ontology design pattern templates were compared with existing templates of other patterns to identify improvement areas. After this, two surveys were conducted with novice users and expert ontology engineers to improve the readability and usability of content ontology design patterns from the user perspective and to discover differences in opinion while using the patterns. Based on the findings of comparison and survey results, we proposed suggestions to improve the current template and presentation of content ontology design patterns.

L'un des challenges des roboticiens consiste à gérer un grand nombre de variabilités. Ces dernières concernent les concepts liés au matériel et aux logiciels du domaine de la robotique. Par conséquent, le développement des applications de robotique est une tâche complexe. Non seulement, elle requiert la maîtrise des détails de bas niveau du matériel et du logiciel mais aussi le changement du matériel utilisé dans une application entraînerait la réécriture du code de celle-ci. L'utilisation de l'ingénierie dirigée par les modèles dans ce contexte est une voie prometteuse pour (1) gérer les problèmes de dépendance de bas niveau des applications des détails de bas niveau à travers des modèles stables et (2) faciliter le développement des applications à travers une génération automatique de code vers des plateformes cibles. Les langages de modélisation spécifiques aux domaines mettent en oeuvre les techniques de l'ingénierie dirigée par les modèles afin de représenter les concepts du domaine et permettre aux experts de celui-ci de manipuler des concepts qu'ils ont l'habitude d'utiliser. Cependant, ces concepts ne sont pas suffisants pour représenter tous les aspects d'une application car ils très généraux. Il faudrait alors s'appuyer sur une démarche pour extraire des abstractions à partir de cas d'utilisations concrets et ainsi définir des abstractions ayant une sémantique opérationnelle. Le travail de cette thèse s'articule autour de deux axes principaux. Le premier axe concerne la contribution à la conception d'un langage de modélisation spécifique au domaine de la robotique mobile (RobotML). Nous extrayons à partir d'une ontologie du domaine les concepts que les roboticiens ont l'habitude d'utiliser pour la définition de leurs applications. Ces concepts sont ensuite représentés à travers une interface graphique permettant la représentation de modèles afin d'assurer une facilité d'utilisation pour les utilisateurs de RobotML. On offre ainsi la possibilité aux roboticiens de représenter leurs scénarios dans des modèles stables et indépendants des plateformes cibles à travers des concepts qu'ils ont l'habitude de manipuler. Une génération de code automatique à partir de ces modèles est ensuite possible vers une ou plusieurs plateformes cibles. Cette contribution est validée par la mise en oeuvre d'un scénario aérien dans un environnement inconnu proposé par l'ONERA. Le deuxième axe de cette thèse tente de définir une approche pour rendre les algorithmes résistants aux changements des détails de ba niveau. Notre approche prend en entrée la description d'une tâche de robotique et qui produit : un ensemble d'abstractions non algorithmiques représentant des requêtes sur l'environnment y compris le robot ou des actions de haut niveau , un ensemble d'abstractions algorithmiques encapsulant un ensemble d'instructions permettant de réaliser une sous-tâche de la tâche étudiée , algorithme générique configurable défini en fonction de ces abstractions. Ainsi, l'impact du changement du matériel et des stratégies définies dans les sous-tâches n'est pas très important. Il suffit d'adapter l'implantation de ces abstractions sans avoir à modifier l'algorithme générique. Cette approche est validée sur six variantes d'une famille d'algorithmes de navigation appelée Bug. / One of the challenges of robotics is to manage a large number of variability. The latter concerns the concepts related to hardware and software in the field of robotics. Therefore, the development of robotic applications is a complex task. Not only it requires mastery of low-level details of the hardware and software but also if we change the used hardware in an application, this would impact the code. The use of model-driven engineering in this context is a promising way to (1) manage low-level dependency problems through stable models and (2) facilitate the development of applications through automatic code generation to target platforms . Domain Specific Modeling Languages implement the model driven engineering technologies to represent the domain concepts and enable experts to manipulate concepts they are used to use. However, these concepts are not sufficient to represent all aspects of an application because they are very general. We would then use an approach to extract abstractions from concrete use cases and thus define abstractions with an operational semantics. The work of this thesis focuses on two main axes. The first concerns the contribution to the design of a domain specific modeling language for mobile robots (RobotML). We extract from a domain ontology concepts that roboticists have used to use to define their applications. These concepts are then represented through a graphical interface representation model to ensure ease of use for RobotML users. An automatic code generation from these models can then be performed to one or more target platforms. This contribution is enabled by setting implement an air scenario, in an unknown environment, proposed by ONERA. The second focus of this thesis attempts to define an approach to make the algorithms resistant to the change of low-level details. Our approach takes as input a description of a task and produces robotic : a set of non-algorithmic abstractions representing queries on environnment (including robot) or high-level actions, a set of algorithmic abstractions encapsulating a set of instructions to perform a sub-task of the studied task, a generic configurable algorithm defined according to these abstractions. Thus, the impact of changing hardware and strategies defined in the sub-tasks is not very important. Simply adapt the implementation of these abstractions without changing the generic algorithm. This approach is validated on six variants of a navigation algorithms family called Bug.

This study is qualitative and interpretive in nature. It examines the perception of 6 people aged 23-32 with decent experience in using the Web on the usability of three user interface website design patterns. These patterns are the ‘hamburger’ icon (an icon used primarily in mobile websites and apps that shows a hidden navigation when clicked), CAPTCHAs (a task that users have to complete to continue browsing a webpage to prevent automated software operating on the webpage) and returning to the homepage. It searches for the characteristics that they desire to see in those three user interface design patterns and the actions that those patterns represent. The participants are reached through interviews and observations and the research pinpoints that although experienced Internet users find the user interface elements relatively usable some usability factors can be worked upon in the chosen design elements and pinpoints what users would want to see changed, the actual changes they want and the problems they actually encounter with the current status of the three (3) design patterns and their usability. More noticeably, the research pinpoints that a “Homepage” button would be more usable than “Home” button which is the de facto standard as of this moment and it shows that the ‘hamburger’ icon is usable enough amongst experienced users, contradicting the research pinpointing that 71 out of 76 fail using the icon (Fichter and Wisniewski, 2016) probably due to the participants’ experience with technology, but other, preferable alternatives to the ‘hamburger’ icon are revealed from the participants which are in line with the current literature. CAPTCHAs are confirmed as a ‘nuisance’ (Pogue, 2012) and the need for CAPTCHAs which are quick to solve emerges which is what forms the perception of usability of the participants.

This dissertation investigates three topics related to movement and events associated with geospatial barriers. This research makes a unique contribution to geographic information science (GIScience), by examining how boundaries influence the interactions of other geographic features and to location-based services by bringing a GIScience perspective to geofence services. Chapters 2, 3, and 4 can be considered independently as journal articles. Each of these chapters builds on the previous. Chapter 2 serves as the base by examining geospatial barriers and impedance events associated with these barriers. The relationships between barriers, the features they protect and the features that they hinder are formalized in an ontology design pattern (ODP) that also includes events associated with these features. Algorithms are written to demonstrate the ODP can be used to answer queries about the presence or absence of barrier events. Chapter 3 transitions from physical boundaries to digital boundaries by examining geofences, a location-based notification service. Interaction between users and multiple geofences are investigated when the configuration of geofences differs (i.e. disconnected, partially overlapping, and completely overlapping) and when geofences are independent or dependent (a rule states that the activation of geofence Y depends on users having visited geofence X). A geofence system is prototyped in an iOS environment and used to further evaluate user-geofence interactions. Chapter 4 expands on the topic of location- based notification regions by investigating what is required for a geofence system to handle events. How changes in conditions (e.g. the spreading of a flood or movement of a fire) interact with geofences and users and what new categories of interactions are required to handle these changes are discussed. The proposed system is applied to a scenario of flooding on multiple rivers interrupting the transportation network.

Patterns provide solutions to recurring design problems in a variety of domains, including that of software design. The best patterns are generative: they show how to build the solution they propose, rather than just explaining it. A collection of patterns that work together to generate a complex system is called a pattern language. Pattern languages have been written for domains as diverse as architecture and computer science, but the process of developing pattern languages is not well understood. This thesis focuses on defining both the structure of pattern languages and the processes by which they are built. The theoretical foundation of the work is existing theory on symmetry breaking. The form of the work is itself a pattern language: a Language Designer's Pattern Language (LDPL). LDPL itself articulates the structure of pattern languages and the key processes by which they form and evolve, and thus guides the building of a properly structured pattern language. LDPL uses multidisciplinary examples to validate the claims made, and an existing software pattern language is analyzed using the material developed. A key assumption of this thesis is that a pattern language is a structural entity; a pattern is not just a transformation on system structure, but also the resultant structural configuration. Another key assumption is that it is valid to treat a pattern language itself as a complex, designed system, and therefore valid to develop a pattern language for building pattern languages. One way of developing a pattern language for building pattern languages would be to search for underlying commonality across a variety of existing, well known pattern languages. Such underlying commonality would form the basis for patterns in LDPL. This project has not directly followed this approach, simply because very few pattern languages that are genuinely structural have currently been explicitly documented. Instead, given that pattern languages articulate structure and behavior of complex systems, this research has investigated existing complex systems theory - in particular, symmetry-breaking - and used that theory to underpin the pattern language. The patterns in the language are validated by examples of those patterns within two well known pattern languages, and within several existing systems whose pattern languages have not necessarily been explicitly documented as such, but the existence of which is assumed in the analysis. In addition to developing LDPL, this project has used LDPL to critique an existing software pattern language, and to show how that software pattern language could potentially have been generated using LDPL. Existing relationships between patterns in the software language have been analyzed and, in some cases, changes to patterns and their interconnections have been proposed as a way of improving the language. This project makes a number of key contributions to pattern language research. It provides a basis for semantic analysis of pattern languages and demonstrates the validity of using a pattern language to articulate the structure of pattern languages and the processes by which they are built. The project uses symmetry-breaking theory to analyze pattern languages and applies that theory to the development of a language. The resulting language, LDPL, provides language developers with a tool they can use to help build pattern languages.

<p>Designmönster är beprövade och återanvändbara designlösningar på återkommande designproblem inom en viss kontext. Designmönster handlar om att inte behöva uppfinna hjulet om och om igen. Designmönster fångar lösningar och kunskap inom mjukvaruutveckling.</p><p>Vi har försökt beskriva och förstå hur IFS och Intentia tar sig an arbetet som omfattas i våra frågeställningar. Våra frågeställningar har varit hur designmönster kan hittas, dokumenteras</p><p>och katalogiseras samt hur designmönster kan spridas till medarbetare.</p><p>Vi har i denna undersökning anslutit oss till de tankegångar som finns inom hermeneutiken och vi har därför valt att använda oss av en kvalitativ metodteori, vars drag ligger mer åt det</p><p>hermeneutiska perspektivet. Vi har genomfört intervjuer med representanter från ovan nämnda företag.</p><p>Undersökningen har visat att bägge företagen har grupper med erfarna utvecklare som finner nya designmönster. IFS dokumenterar inte sina mönster medan Intentia gör det, men dock inte enligt någon standard. Dokumenten katalogiseras på ett intranät. IFS katalogiserar inte sina</p><p>mönster, men de kanske kommer att kategoriseras utifrån sin funktionella tillhörighet. Intentia kategoriserar sina designmönster utifrån vilken typ av designmönster det är fråga om. Varje</p><p>designmönster hör till en viss grupp av designmönster. De katalogiserar ett designmönster där liknande designmönster finns. När det gäller spridningen av designmönster till medarbetarna inom företagen så hävdar IFS att själva kunskapsöverföringen i deras utvecklingsmiljö. Intentia menar att de erfarna utvecklarna i gruppen som hittar nya mönster även är skickliga på att förmedla designmönster till andra utvecklare i organisationen.</p>

Web application design is a broad term that refers to any aspect of designing a Web application, including designing Web interfaces to data. There are a number of commercial software tools available that employ various techniques for implementing Web access to databases. However, these techniques apply only to portions of Web application implementation and lack a common design paradigm. We believe that defining an approach to designing and implementing Web applications based on views, frameworks, and patterns allows us to extend an object-oriented design representation and develop reusable and extensible design solutions for a class of Web applications in which the concerns are separated. The major contribution of this thesis is the development of a new approach to designing Web applications, producing the following visible contributions: a model for Web applications based upon a separation of concerns using views; a framework for system elements so that object-oriented design patterns can be used to build the application; a reusable design approach so that many Web applications can be built around the same framework; a coherent and organized framework representation using extended UML; and an implementation approach that can be implemented on a number of different platforms using a range of software and tools. In support of this solution, this thesis shows the design and implementation of a proof-of-concept Web application using this design technique. We believe that the approach to Web application design promoted in this thesis has proven itself useful in a practical way for the case studies discussed herein and points the way to a wider range of design and implementation possibilities.

Designmönster är beprövade och återanvändbara designlösningar på återkommande designproblem inom en viss kontext. Designmönster handlar om att inte behöva uppfinna hjulet om och om igen. Designmönster fångar lösningar och kunskap inom mjukvaruutveckling. Vi har försökt beskriva och förstå hur IFS och Intentia tar sig an arbetet som omfattas i våra frågeställningar. Våra frågeställningar har varit hur designmönster kan hittas, dokumenteras och katalogiseras samt hur designmönster kan spridas till medarbetare. Vi har i denna undersökning anslutit oss till de tankegångar som finns inom hermeneutiken och vi har därför valt att använda oss av en kvalitativ metodteori, vars drag ligger mer åt det hermeneutiska perspektivet. Vi har genomfört intervjuer med representanter från ovan nämnda företag. Undersökningen har visat att bägge företagen har grupper med erfarna utvecklare som finner nya designmönster. IFS dokumenterar inte sina mönster medan Intentia gör det, men dock inte enligt någon standard. Dokumenten katalogiseras på ett intranät. IFS katalogiserar inte sina mönster, men de kanske kommer att kategoriseras utifrån sin funktionella tillhörighet. Intentia kategoriserar sina designmönster utifrån vilken typ av designmönster det är fråga om. Varje designmönster hör till en viss grupp av designmönster. De katalogiserar ett designmönster där liknande designmönster finns. När det gäller spridningen av designmönster till medarbetarna inom företagen så hävdar IFS att själva kunskapsöverföringen i deras utvecklingsmiljö. Intentia menar att de erfarna utvecklarna i gruppen som hittar nya mönster även är skickliga på att förmedla designmönster till andra utvecklare i organisationen.