Tesis sobre el tema "Content Ontology Design Patterns"

Ontologies are formal knowledge models that describe concepts and relationships and enable data integration, information search, and reasoning. Ontology Design Patterns (ODPs) are reusable solutions intended to simplify ontology development and support the use of semantic technologies by ontology engineers. ODPs document and package good modelling practices for reuse, ideally enabling inexperienced ontologists to construct high-quality ontologies. Although ODPs are already used for development, there are still remaining challenges that have not been addressed in the literature. These research gaps include a lack of knowledge about (1) which ODP features are important for ontology engineering, (2) less experienced developers' preferences and barriers for employing ODP tooling, and (3) the suitability of the eXtreme Design (XD) ODP usage methodology in non-academic contexts. This dissertation aims to close these gaps by combining quantitative and qualitative methods, primarily based on five ontology engineering projects involving inexperienced ontologists. A series of ontology engineering workshops and surveys provided data about developer preferences regarding ODP features, ODP usage methodology, and ODP tooling needs. Other data sources are ontologies and ODPs published on the web, which have been studied in detail. To evaluate tooling improvements, experimental approaches provide data from comparison of new tools and techniques against established alternatives. The analysis of the gathered data resulted in a set of measurable quality indicators that cover aspects of ODP documentation, formal representation or axiomatisation, and usage by ontologists. These indicators highlight quality trade-offs: for instance, between ODP Learnability and Reusability, or between Functional Suitability and Performance Efficiency. Furthermore, the results demonstrate a need for ODP tools that support three novel property specialisation strategies, and highlight the preference of inexperienced developers for template-based ODP instantiation---neither of which are supported in prior tooling. The studies also resulted in improvements to ODP search engines based on ODP-specific attributes. Finally, the analysis shows that XD should include guidance for the developer roles and responsibilities in ontology engineering projects, suggestions on how to reuse existing ontology resources, and approaches for adapting XD to project-specific contexts.

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.

XDtools is a plugin originally used in the NeOn Toolkit ontology editor. XDtools is used as a tool for the ontology engineer when designing new ontologies or to add new parts to existing ontologies. The XDtools plugin was partially ported to another ontology editor, Protégé. This thesis describes the implementation and design choices made during the work with porting the plugin. A description of the parts that have been ported can be found in the report. It also contains the result of the testing and user study made after the implementation. Conclusions of those results and proposed changes to the plugin are also found in the report.

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Dey et al. [10] define context as the information set that can be used to characterize the status of an entity (e.g. person, place or object relevant to the user-application interaction). Perera et al. [36] propose a context information life cycle in 4 phases: acquisition, modeling, reasoning and dissemination. Context modeling consists in representing the real world in computing and, according to Bettini et al. [2], a good information context modeling mitigates the complexity of context-aware applications. In the context of this work, a systematic review demonstrated that the literature has focused on context information modeling, but with less emphasis on the architectural project. The main problem addressed on this work is the creation and evaluation of architectural projects that work together on the context modeling phase of a Semantic Context-Aware System (SCAS), which uses ontologies as main information modeling technique. This work proposes an architectural solution to two relevant services of the ontology-based context modeling phase: the former represents context information collected through sensors, and the latter aggregates context information represented by the former for a same individual or entity. Both architectural designs were built using well-known architectural styles and design patterns, as well as were evaluated against architectural designs of similar projects. As a result, the main contributions include the architectural designs of ontology-based services for context representation and aggregation as references for the development of SCAS in terms of the context modeling phase.
Contexto é o conjunto de informações que pode ser utilizado para caracterizar a situação de uma entidade (pessoa, lugar ou objeto relevante para a interação usuário-aplicação) [10]. Perera et al. [36] propõem um ciclo de vida para a informação de contexto composto por 4 etapas: aquisição, modelagem, raciocínio e disseminação. A etapa de modelagem de contexto consiste em representar o mundo real na computação. Segundo Bettini et. al. [2] “uma boa modelagem de informação de contexto reduz a complexidade das aplicações sensíveis a contexto”. Um Sistema Sensível ao Contexto Semântico (SSCS) é um sistema computacional que utiliza ontologias que, segundo Gruber [15], é “uma especificação explícita de uma conceitualização”, e consistem em uma das formas de modelar as informações de contexto. Como resultado de uma revisão sistemática feita pelo autor deste trabalho evidenciou que na literatura o foco dos trabalhos tem sido na modelagem da informação de contexto com menor enfoque no uso de projeto arquitetural. Com base nisso, o principal problema endereçado neste trabalho é a criação e avaliação dos projetos arquiteturais que trabalhem em conjunto na modelagem do ciclo de vida de contexto em SSCS. Objetiva-se elaborar uma solução arquitetural para sistemas sensíveis ao contexto semântico baseado em ontologias. Propôs-se neste trabalho o projeto arquitetural para o software de representação ontológica de contexto e para o software de agregação ontológica de contexto. O primeiro representa as informações coletadas através de sensores e o segundo agrega as informações representadas para um mesmo indivíduo ou entidade. Realizou-se, assim, a avaliação dos projetos arquiteturais propostos e explana-se sobre os resultados obtidos, comparando-os com outros projetos existentes na literatura. Com a obtenção dos resultados propostos, espera-se contribuir com a literatura, apresentando projetos arquiteturais e avaliações destes, auxiliando, assim, o desenvolvimento de SSCS no que se refere à modelagem do ciclo de vida de contexto.

Knowledge Representation (KR) languages such as OWL (Web Ontology Languge), having precise semantics, offer the possibility of computationally exploiting biological knowledge, by codifying it in the axioms of bio-ontologies widely used in life sciences for knowledge management. Knowledge is, however, often represented in bio-ontologies without following rigorous principles of modelling and the resulting bio-ontologies are axiomatically lean. Therefore knowledge cannot be computationally exploited for integrity checking, hypothesis generation, consistency maintenance, integration, or rich querying. A solution that can contribute to the rigorous modelling and axiomatic richness of bio-ontologies is is the use of Ontology Design Patterns (ODPs). ODPs are thoroughly documented and efficient solutions for recurrent problems encountered when building ontologies. Therefore ODPs act as guides on how to use KR languages for creating ontology fragments that have well known advantages and side effects. In order forr ODPs to be efficiently accessed by bio-ontologists, an online catalogue of ODPs has been created, describing different ODPs using a consisistent documentation schema. Such ODPs, apart from being accessed, can be applied automatatically with the Ontology Preprocessor Language (OPPL), as OPPL makes it possible to encapsulate ODPs in scripts to be executed on OWL ontologies, making the application of ODPs replicable and flexible. The infrastructure for applying ODPs formed by the catalogue amd OPPL has been used for applying ODPs in bio-ontologies like the Cell Type Ontology. The results of such application have been evaluated to assess the applied ODPs and the chang on ontology quality.

This thesis explores a very recurrent modeling scenario in ontology design that deals with the notion of real world concepts that can be classified according to multiple criteria. Current ontology modeling guidelines do not explicitly consider this aspect in the representation of such concepts. Such void leaves ample room for ad-hoc practices that can lead to unexpected or undesired results in ontology artifacts. The aim is to identify best practices and design patterns to represent such concepts in OWL DL ontologies suitable for deployment in the Web of Data and the Semantic Web. To assist with these issues, an initial set of basic design guidelines is put forward, that mitigates the opportunity for ad-hoc modeling decisions in the development of ontologies for the problem scenario described. These guidelines relies upon an existing simplified methodology for facet analysis from the field of Library and Information Science. The outcome of this facet analysis produces a Faceted Classification Scheme (FCS) for the concept in question where in most cases a facet would correspond to a classification criterion. The Value Partition, the Class As Property Value and the Normalisation Ontology Design Patterns (ODPs) are revisited to produce an ontology representation of a FCS. A comparative analysis between a FCS and the Normalisation ODP in particular, revealed the existence of key similarities between the elements in the generic structure of both knowledge representation paradigms. These similarities allow to establish a series of mappings to transform a FCS into an OWL DL ontology that contains a valid representation of the classification criteria involved in the characterization of the domain concept. An existing FCS example in the domain of \Dishwasher Detergent" and existing ontology examples in the domain of \Pizza", \Wine" and \Fault" (in the context of a computer system) are used to illustrate the outcome of this research

A Content Management System (CMS) is a software application for creating, publishing, editing and managing content. The future step in content management system development is building intelligence over existing content resources that are heterogeneous in nature. Intelligence collected at the knowledge base can later on be used for executing semantic queries. Expressing the relations among content resources with ontological formalisms is therefore the key to implementing such semantic features. In this work, a methodology for the semantic lifting of JSR-170 compliant content repositories to ontologies is devised. The fact that in the worst case JSR-170 enforces no particular structural restrictions on the content model poses a technical challenge both for the initial build-up and further synchronization of the knowledge base. To address this problem, some recurring structural patterns in JSR-170 compliant content repositories are exploited. The value of the ontology extraction framework is assessed through a semantic search mechanism that is built on top of the extracted ontologies. The work in this thesis is complementary to the &ldquo
Interactive Knowledge Stack for small to medium CMS/KMS providers (IKS)&rdquo
project funded by the EC (FP7-ICT-2007-3).

Procedural content generation (PCG) can be a useful tool for aiding creativityand efficiency in the process of designing game levels. Mixed-initiative level genera-tion tools where a designer and an algorithm collaborate to iteratively generate gamelevels have been used for this purpose – taking advantage of the combination of com-putational efficiency and human intuition and creativity. However, it can be difficultfor designers to work with tools that do not respond to the common language of games:game design patterns.It has been demonstrated that game design patterns can be integrated into PCGalgorithms, but formally-defined and hierarchically-arranged game design patternshave not yet been used as a means of increasing gameplay-based control in mixed-initiative dungeon generators. We present a method for evolving dungeon rooms usingmulti-level game design patterns in the objective function of a genetic algorithm, aswell as an instantiation of this method in a mixed-initiative dungeon design tool. Ourresults show that we are able to control the frequency and type of design patterns ingenerated rooms using pattern-related input parameters, enabling us to create dungeonrooms containing a wide variety of patterns on different levels of abstraction.Results from a small-scale user study of professional game developers suggest thatthe use of game design patterns in mixed-initiative level design tools can be a promisingway of providing a good starting point when designing a level, as well as offeringmeaningful gameplay related feedback throughout the design process. We also identifychallenges that will need to be faced if game design pattern-based mixed-initiative leveldesign tools are to become a part of the game designer’s toolkit.

Les événements indésirables (EIs) sont devenus une vraie préoccupation du monde médical, leur réduction étant recherchée pour assurer la meilleure sécurité possible pour les patients. Les EIs sont, selon la HAS, ‘‘ des situations qui s'écartent de procédures ou de résultats escomptés dans une situation habituelle et qui sont ou qui seraient potentiellement sources de dommages’’. Alors que les EIs postopératoires sont étudiés depuis de nombreuses années, ceux ayant lieu au cours des opérations ne le sont que depuis récemment, comme le montre la récente classification des EIs intraopératoires par Kaafarani et al. publié en 2014. Cependant, la classification d'EIs intraopératoires n'est que la première étape pour comprendre les comportements chirurgicaux qui les entraînent.Dans cette thèse, nous présenterons des méthodes pour détecter l'apparition de déviations dues à l'apparition d'EIs intraopératoires et pour identifier des comportements chirurgicaux à partir de modèle de processus chirurgicaux.Ce travail a nécessité de concevoir et développer une modélisation formelle de la rectopexie et des événements indésirables qui sont associés à cette procédure chirurgicale grâceà la mise en place d'ontologies. Cette modélisation formelle nous a permis de bien appréhender le principe de cette opération et de fournir un vocabulaire permettant une annotation détaillé de vidéos endoscopiques de rectopexies, afin de créer des modèles de processus chirurgicaux en jeu.Grâce à l'annotation des vidéos chirurgicales basée sur cette modélisation, nous avons développé une une méthode de détection automatique des déviations dues à l'apparition d'événements indésirables Cette méthode est basée sur un alignement temporel non-linéaire multi-dimensionnel, que nous avons développé, suivi d'un modèle semi-Markovien caché que nous avons entraîné pour déterminer s'il existe des déviations par rapport à une chirurgie de référence et si celles-ci sont dues à des événements indésirables.Cette détection de déviations dues aux événements indésirables est la première étape afin de comprendre les raisons de leurs apparitions. Nous émettons l'hypothèse que leurs apparitions peuvent être expliquées par une succession d’activités, c'est-à-dire un pattern. Pour répondre à cette hypothèse, nous avons mis en place une méthode de découverte de patterns permettant d'identifier les comportements chirurgicaux spécifiques à différents critères. Cette identification de comportements chirurgicaux est réalisée par une classification ascendante hiérarchique avec la mise en place d'une nouvelle métrique basée sur les patterns partagés entre les chirurgies. Afin de valider notre méthode, nous l'avons comparé à deux études mettant en évidence des différences de comportements chirurgicaux, comme par exemple entre différents sites chirurgicaux ou entre deux types de procédure de la même opération. Une fois la méthode validée, nous avons utilisé notre méthode afin de montrer s'il existait des comportements chirurgicaux spécifiques à des données préopératoires et à l'apparition d'événements indésirables.Pour finir, nous revenons sur les contributions les plus importantes de ces travaux à travers une discussion générale et nous proposons différentes pistes pour améliorer nos résultats
L'auteur n'a pas fourni de résumé en anglais

Avec le déclin grandissant des prises de pêches, une augmentation de la production piscicole est attendue pour les prochaines années. Cependant, de nombreux problèmes de reproduction sont observés dans les élevages, principalement une mortalité élevée au début de la vie. Cela concerne principalement des espèces piscicoles pour lesquelles le processus de domestication commence. Mon travail de thèse a visé à mieux comprendre et potentiellement aider à améliorer les performances de reproduction en étudiant le contenu transcriptomique des œufs de perche commune (Perca fluviatilis) en lien avec leur qualité. Ces résultats participent à la compréhension des mécanismes moléculaires impliqués dans la mortalité embryonnaire précoce. Cette espèce, en cours de domestication, revêt une grande importance dans le contexte de la diversification des espèces d’intérêt aquacole en Europe continentale. J’ai utilisé des analyses par puce à ADN et RT-qPCR pour caractériser les profils d'expression génique dans les œufs de perche de qualité variables. Les expériences ont été menées dans deux contextes scientifiques. Dans un premier temps, j’ai comparé l’effet des méthodes d’évaluation de la qualité des œufs sur les résultats transcriptomiques obtenus. Ainsi, les œufs ont été classés dans des groupes de qualité (bonne ou mauvaise) en utilisant divers critères liés au développement embryonnaire (taux de survie, taux de malformation) et divers seuils limites pour borner ces groupes. L’utilisation de critères de survie embryonnaire précoces a permis d'identifier des profils d'expression génique distincts entre les groupes de qualité. Cependant, le nombre et la nature des gènes exprimés de manière différentielle (DEG) étaient variables. Un seul gène était exprimé de manière différentielle dans toutes les analyses, quelles que soient les conditions. Cela montre à quel point les résultats transcriptomiques sont sensibles aux méthodes d’évaluation qui doivent être sérieusement pris en compte en amont de comparaisons intra et inter-espèces. Dans un deuxième temps, j’ai comparé le contenu transcriptomique d’œufs de femelles avec des histoires de domestication différentes. Dans cette étude, les femelles les plus proches des populations sauvages présentaient une meilleure qualité d'œufs. En outre, deux modèles distincts d'expression génique ont été observés et plus de 300 DEG ont été identifiés entre les populations. Étant donné que les causes de la variabilité élevée des performances de reproduction des espèces en cours de domestication sont mal connues, cette découverte pourrait ouvrir de nouvelles hypothèses d’investigation. Enfin, il devenait important de déterminer le moment où le gène identifié dans les approches précédentes soutiendrait exclusivement le développement embryonnaire précoce. Dans ce but, une étude préliminaire a permis de faire une première évaluation de l’activation du génome zygotique (ZGA) chez cette espèce. L’ensemble de ces résultats ouvre la voie vers l’établissement de nouvelles méthodes d’investigation de la qualité des gamètes chez la perche commune. Ces méthodes permettront de faire des études précises de l’évolution du succès de développement à chaque génération au cours d’un processus de domestication. Des méthodes similaires pourraient être établies chez d’autres espèces en prenant en compte leurs particularités. Il serait alors intéressant de tenter d’étudier des espèces présentant des caractères communs ou divergents. Nous pourrons alors tenter de comprendre les régulations propres à chaque espèce ou au contraire largement retrouvés chez plusieurs espèces de poisson
In the aquaculture context, increase on production are expected for the next years and yet, many reproductive issues are reported, including high mortality during early life stages. It concerns mostly species for which the domestication process is at the very beginning. My PhD work aimed at better understanding and potentially helping improving reproductive performance by investigating eggs the transcriptomic content of the Eurasian perch (Perca fluviatilis) eggs in association with their quality which may constitute one of the sources for embryonic mortality. Eurasian perch is a species, in process of domestication, with strong importance for aquaculture diversification in inland Europe. We employed microarray and RT-qPCR analyses to characterize gene expression patterns of Eurasian perch eggs presenting different potential to develop properly after fertilization. The experiments were conducted in two scientific contexts. In the first one, different methods to access egg quality were employed and their potential impacts on the transcriptomic results were evaluated. Therefore, when eggs were classified into the respective quality groups (high or low) using early embryonic survival as criteria, we were always able to identify distinct patterns of gene expression between quality groups. However, the number and nature of the differentially expressed genes (DEG) were variable and only one gene was commonly differentially expressed no matter the methods employed. This shows how transcriptomic results are sensitive to methods and should be deeply considered for intra- and inter-species comparisons. The second context consisted of investigating whether females presenting different histories of domestication would differ in their eggs mRNA content, and how it affects egg quality. In this study, females closest to wild populations presented better egg quality. In addition, two distinct patterns of gene expression were observed and more than 300 DEG were identified between populations. Because not much is known about the causes of high variability in reproductive performance in species in process of domestication, this finds could open new hypothesis of investigation. Finally, it became important to determine the moment until which the gene identified in the previous approaches were exclusively supporting embryonic early development. With this purpose, a preliminary study allowed making a first evaluation of the zygotic genome activation (ZGA) in this species. As a whole, this study identified numerous maternal-effect genes which implication in embryos early development should be further investigated. In addition, these results suggest that more comparable methods to investigate egg quality in Eurasian perch could be established. These methods will make possible more precise studies in the variation of the development success under the influence of distinc factors, such the domestication process. Similar methods could also be established in other species considering their own common or divergent characters. It would help understanding molecular mechanisms species specific or widely found in finfish species

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.

Software engineers use design patterns to refactor software models for quality. This displaces domain patterns and makes software hard to maintain. Detecting design patterns directly in requirements can circumvent this problem. To facilitate the analogical transfer of patterns from problem domain to solution model however we must describe patterns in ontological rather than in technical terms. In a first study novice designers used both pattern cases and a pattern ontology to detect design ideas and patterns in requirements. Errors in detection accuracy led to the revision of the pattern ontology and a second study into its pattern-discriminating power. Study results demonstrate that pattern ontology is superior to pattern cases in assisting novice software engineers in identifying patterns in the problem domain.

This dissertation addresses the challenge of improving automatic level generation processes for plat-form videogames. As Procedural Content Generation (PCG) techniques evolved from the creation of simple elements to the construction of complete levels and scenarios, the principles behind the generation algorithms became more ambitious and complex, representing features that beforehand were only possible with human design. PCG goes beyond the search for valid geometries that can be used as levels, where multiple challenges are represented in an adequate way. It is also a search for user-centred design content and the creativity sparks of humanly created content. In order to improve the creativity capabilities of such generation algorithms, we conducted part of our research directed to the creation of new techniques using more ambitious design patterns. For this purpose, we have implemented two overall structure generation algorithms and created an addi-tional adaptation algorithm. The later can transform simple branched paths into more compelling game challenges by adding items and other elements in specific places, such as gates and levers for their activation. Such approach is suitable to avoid excessive level linearity and to represent certain design patterns with additional content richness. Moreover, content adaptation was transposed from general design domain to user-centred principles. In this particular case, we analysed success and failure patterns in action videogames and proposed a set of metrics to estimate difficulty, taking into account that each user has a different perception of that concept. This type of information serves the generation algorithms to make them more directed to the creation of personalised experiences. Furthermore, the conducted research also aimed to the integration of different techniques into a common ground. For this purpose, we have developed a general framework to represent content of platform videogames, compatible with several titles within the genre. Our algorithms run over this framework, whereby they are generic and game independent. We defined a modular architecture for the generation process, using this framework to normalise the content that is shared by multiple modules. A level editor tool was also created, which allows human level design and the testing of automatic generation algorithms. An adapted version of the editor was implemented for the semi-automatic creation of levels, in which the designer may simply define the type of content that he/she desires, in the form of quests and missions, and the system creates a corresponding level structure. This materialises our idea of bridging human high-level design patterns with lower level automated generation algorithms. Finally, we integrated the different contributions into a game prototype. This implementation allowed testing the different proposed approaches altogether, reinforcing the validity of the proposed archi-tecture and framework. It also allowed performing a more complete gameplay data retrieval in order to strengthen and validate the proposed metrics regarding difficulty perceptions.