In the computationally intensive and diverse scientific environment of geosciences, substantial volumes of data are generated by specialized complex processing systems called ‘models’. These datasets contain little knowledge of their processing. Therefore a high degree of domain expertise is required to interpret, regenerate and tweak their production. Provenance is described as a general ability to record and evolve information related to the creation of data. We extend this idea further by proposing a mechanism by which a model’s setup and its domain semantics are integrated with the data it produces. This creates a scope for controlling model executions using their respective setups or ‘configurations’. In this work we created an application neutral framework which can be applied to models of a similar class in geosciences. Our objective is to allow scientists to share their experiments with anyone having an interest in it while allowing for formally controlled and extensible customizations.

Informação sobre o estágio de câncer num paciente é fundamental quando médicos avaliam o progresso de seu tratamento. A determinação do estágio de câncer (cancer staging) é um processo que leva em consideração a descrição, localização, características e possíveis metástases dos tumores cancerosos de um paciente. Esse processo deve seguir um padrão de classificação como, por exemplo, o padrão TNM. Porém, na prática clínica, a execução desse processo pode ser tediosa, propensa a erros e gerar incertezas. Com o intuito de amenizar esses problemas, este trabalho tem como objetivo auxiliar radiologistas fornecendo uma segunda opinião na avaliação do estágio de câncer de um paciente. Para isso, tecnologias da Web Semântica, como ontologias e reasoning, foram usadas para classificar automaticamente estágios de câncer. Essa classificação usou anotações semânticas feitas por radiologistas, usando a ferramenta ePAD, e armazenadas no formato AIM. Um protótipo de classificador, baseado no padrão TNM, foi criado. Ele transforma anotações AIM em indivíduos da ontologia AIM4-O e, usando axiomas e regras (escritos na linguagens OWL-SWRL) representando o padrão TNM, ele automaticamente calcula o estágio de câncer de fígado de pacientes. A ontologia AIM4-O foi desenvolvida, como parte desse trabalho, para representar anotações AIM 4 em OWL. Esse classificador TNM foi avaliado, usando-se dados reais de relatórios radiológicos de pacientes do NCIs Genomic Data Commons (GDC), em termos de precisão e revocação, com resultados respectivos de 85,7% e 81,0% (quando comparado aos valores reais de estágio de câncer dos relatórios). Todo o processo foi validado com radiologistas do Radiology Dept. of the Stanford University. / Information about cancer staging in a patient is crucial when clinicians assess treatment progress. Determining cancer stage is a process that takes into account the description, location, characteristics and possible metastasis of cancerous tumors in a patient. It should follow classification standards, such as the TNM Classification of Malignant Tumors. However, in clinical practice, the implementation of this process can be tedious, error-prone and create uncertainty. In order to alleviate these problems, we intend to assist radiologists by providing a second opinion in the evaluation of cancer stage in patients. For doing this, Semantic Web technologies, such as ontologies and reasoning, were used to automatically classify cancer stages. This classification used semantic annotations made by radiologists, using the ePAD tool, and stored using standard AIM format. A TNM based classifier prototype was created. It transforms AIM annotations in AIM4- O ontology individuals and, using axioms and rules (written in OWL-SWRL languages) representing the TNM standard, it automatically calculates patients liver cancer stage. The AIM4-O ontology was developed, as part of this work, to represent AIM 4 annotations in OWL. This TNM classifier was evaluated, using real patients radiology reports, from the NCIs Genomic Data Commons (GDC), in term of precision and recall, with 85.7% and 81.0% respective results (when compared to the actual cancer stages from the reports). The whole process was validated with radiologists from the Radiology Dept. of the Stanford University.

Le sujet de cette thèse de doctorat consiste à proposer une architecture ambiante d’interaction homme-robot-environnement. Dans le cadre de la robotique d’aide à la personne dépendante. Cette architecture va permettre aux robots « Ubiquitous Networked Robots » de prendre en compte le contexte évolutif pour fournir continuellement du service à l'utilisateur. L'architecture proposée utilise le concept d'Ontologie du domaine pour la description de l'environnement. Nous avons choisi d'utiliser l'outil open source PROTEGE qui va nous permettre de définir l'ontologie ainsi que les moteurs de fusion et de fission. Les entrées multimodales seront fusionnées puis subdivisées en tâches élémentaires et envoyées comme commandes au fauteuil roulant muni d'un bras manipulateur. Cette architecture sera validée par des spécifications et des simulations via des réseaux de Pétri temporels et stochastiques. / The subject of this thesis is to provide an ambient architecture for the human-robotenvironment interaction, as part of thedependent person robotics help. This architecture will enable the robot to take into account the changing context and continually provide a service to the user. The architecture uses the concept of ontology for the descriptionof the environment. We have chosen to use the open source PROTEGE because it allows the definition of the ontology and the fusion and fission engines. Indeed, multimodal inputs will be merged and subdivided into elementary tasks and sent tocontrol the wheelchair with the manipulated arm. This architecture will be validated by specifications and simulations via temporal and stochastic Petri nets.

Informação sobre o estágio de câncer num paciente é fundamental quando médicos avaliam o progresso de seu tratamento. A determinação do estágio de câncer (cancer staging) é um processo que leva em consideração a descrição, localização, características e possíveis metástases dos tumores cancerosos de um paciente. Esse processo deve seguir um padrão de classificação como, por exemplo, o padrão TNM. Porém, na prática clínica, a execução desse processo pode ser tediosa, propensa a erros e gerar incertezas. Com o intuito de amenizar esses problemas, este trabalho tem como objetivo auxiliar radiologistas fornecendo uma segunda opinião na avaliação do estágio de câncer de um paciente. Para isso, tecnologias da Web Semântica, como ontologias e reasoning, foram usadas para classificar automaticamente estágios de câncer. Essa classificação usou anotações semânticas feitas por radiologistas, usando a ferramenta ePAD, e armazenadas no formato AIM. Um protótipo de classificador, baseado no padrão TNM, foi criado. Ele transforma anotações AIM em indivíduos da ontologia AIM4-O e, usando axiomas e regras (escritos na linguagens OWL-SWRL) representando o padrão TNM, ele automaticamente calcula o estágio de câncer de fígado de pacientes. A ontologia AIM4-O foi desenvolvida, como parte desse trabalho, para representar anotações AIM 4 em OWL. Esse classificador TNM foi avaliado, usando-se dados reais de relatórios radiológicos de pacientes do NCIs Genomic Data Commons (GDC), em termos de precisão e revocação, com resultados respectivos de 85,7% e 81,0% (quando comparado aos valores reais de estágio de câncer dos relatórios). Todo o processo foi validado com radiologistas do Radiology Dept. of the Stanford University. / Information about cancer staging in a patient is crucial when clinicians assess treatment progress. Determining cancer stage is a process that takes into account the description, location, characteristics and possible metastasis of cancerous tumors in a patient. It should follow classification standards, such as the TNM Classification of Malignant Tumors. However, in clinical practice, the implementation of this process can be tedious, error-prone and create uncertainty. In order to alleviate these problems, we intend to assist radiologists by providing a second opinion in the evaluation of cancer stage in patients. For doing this, Semantic Web technologies, such as ontologies and reasoning, were used to automatically classify cancer stages. This classification used semantic annotations made by radiologists, using the ePAD tool, and stored using standard AIM format. A TNM based classifier prototype was created. It transforms AIM annotations in AIM4- O ontology individuals and, using axioms and rules (written in OWL-SWRL languages) representing the TNM standard, it automatically calculates patients liver cancer stage. The AIM4-O ontology was developed, as part of this work, to represent AIM 4 annotations in OWL. This TNM classifier was evaluated, using real patients radiology reports, from the NCIs Genomic Data Commons (GDC), in term of precision and recall, with 85.7% and 81.0% respective results (when compared to the actual cancer stages from the reports). The whole process was validated with radiologists from the Radiology Dept. of the Stanford University.

Information freely generated, widely distributed and openly interpreted is a rich source of creative energy in the digital age that we live in. As we move further into this irrevocable relationship with self-growing and actively proliferating information spaces, we are also finding ourselves overwhelmed, disheartened and powerless in the presence of so much information. We are at a point where, without domain familiarity or expert guidance, sifting through the copious volumes of information to find relevance quickly turns into a mundane task often requiring enormous patience. The realization of accomplishment soon turns into a matter of extensive cognitive load, serendipity or just plain luck. This dissertation describes a theoretical framework to analyze user interactions based on mental representations in a medium where the nature of the problem-solving task emphasizes the interaction between internal task representation and the external problem domain. The framework is established by relating to work in behavioral science, sociology, cognitive science and knowledge engineering, particularly Herbert Simon’s (1957; 1989) notion of satisficing on bounded rationality and Schön’s (1983) reflective model. Mental representations mediate situated actions in our constrained digital environment and provide the opportunity for completing a task. Since assistive aids to guide situated actions reduce complexity in the task environment (Vessey 1991; Pirolli et al. 1999), the framework is used as the foundation for developing mediating structures to express the internal, external and mental representations. Interaction aids superimposed on mediating structures that model thought and action will help to guide the “perpetual novice” (Borgman 1996) through the vast digital information spaces by orchestrating better cognitive fit between the task environment and the task solution. This dissertation presents an ontology centric architecture for mediating interactions is presented in a semantic web based e-commerce environment. The Design Science approach is applied for this purpose. The potential of the framework is illustrated as a functional model by using it to model the hierarchy of tasks in a consumer decision-making process as it applies in an e-commerce setting. Ontologies are used to express the perceptual operations on the external task environment, the intuitive operations on the internal task representation, and the constraint satisfaction and situated actions conforming to reasoning from the cognitive fit. It is maintained that actions themselves cannot be enforced, but when the meaning from mental imagery and the task environment are brought into coordination, it leads to situated actions that change the present situation into one closer to what is desired. To test the usability of the ontologies we use the Web Ontology Language (OWL) to express the semantics of the three representations. We also use OWL to validate the knowledge representations and to make rule-based logical inferences on the ontological semantics. An e-commerce application was also developed to show how effective guidance can be provided by constructing semantically rich target pages from the knowledge manifested in the ontologies.

Les réseaux à base de politiques (PBN) définissent un paradigme des plus prometteurs pour la gestion et le contrôle des ressources réseaux. COPS tend à être le protocole de facto pour l'utilisation de ce type d'applications. La question se pose de savoir comment déployer ce type de services pour permettre les échanges entre les différentes entités protocolaires du réseau (PEP et PDP). C'est à ce niveau que nous proposons de faire intervenir la notion de réseaux actifs, vu que ce paradigme permet d'intégrer du code exécutable aux paquets transférés et/ou nœuds en vue de distribuer et de configurer dynamiquement les services du réseau. D'autre part, une grande effervescence existe actuellement autour du déploiement des Web services sur Internet à l'aide du protocole SOAP. Toujours dans le cadre de l'Internet mais selon une perspective différente, la représentation sémantique des données, et grâce à la définition d'ontologies, permet aux logiciels d'interpréter intelligemment les données qu'elles gèrent et de ne plus jouer le rôle de simple équipement de stockage passif. La synergie entre les 4 paradigmes: PBN, Réseaux actifs, Web services, et représentation sémantique des données, présente une solution intégrée et portable des plus intéressantes pour la représentation des nœuds de l'architecture active, la conception, l'implémentation et le déploiement de services, et plus spécifiquement un service de gestion dynamique contrôlable et intelligent, dont les données (politiques et règles) sont représentés par une même ontologie.

Family history research on the web is increasing in popularity, and many competing genealogical websites host large amounts of data-rich, unstructured, primary genealogical records. It is labor-intensive, however, even after making these records machine-readable, for humans to make these records easily searchable. What we need are computer tools that can automatically produce indices and databases from these genealogical records and can automatically identify individuals and events, determine relationships, and put families together. We propose here a possible solution—specialized ontologies, built specifically for extracting information from primary genealogical records, with expert logic and rules to infer genealogical facts and assemble relationship links between persons with respect to the genealogical events in their lives. The deliverables of this solution are extraction ontologies that can extract from parish or town records, annotated versions of original documents, data files of individuals and events, and rules to infer family relationships from stored data. The solution also provides for the ability to query over the rules and data files and to obtain query-result justification linking back to primary genealogical records. An evaluation of the prototype solution shows that the extraction has excellent recall and precision results and that inferred facts are correct.

Dans un environnement collaboratif de développement de produit, plusieurs acteurs, ayant différents points de vue et intervenant dans plusieurs phases du cycle de vie de produit, doivent communiquer et échanger des connaissances entre eux. Ces connaissances, existant sous différents formats hétérogènes, incluent potentiellement plusieurs concepts tels que l’historique de conception, la structure du produit, les features, les paramètres, les contraintes, et d’autres informations sur le produit. Les exigences industrielles de réduction du temps et du coût de production nécessitent l’amélioration de l’interopérabilité sémantique entre les différents processus de développement afin de surmonter ces problèmes d’hétérogénéité tant au niveau syntaxique, structurel, que sémantique. Dans le domaine de la CAO, la plupart des méthodes existantes pour l’échange de données d’un modèle de produit sont, effectivement, basées sur le transfert des données géométriques. Cependant, ces données ne sont pas suffisantes pour saisir la sémantique des données, telle que l’intention de conception, ainsi que l’édition des modèles après leur échange. De ce fait, nous nous sommes intéressés à l’échange des modèles « intelligents », autrement dit, définis en termes d’historique de construction, de fonctions intelligentes de conception appelées features, y compris les paramètres et les contraintes. L’objectif de notre thèse est de concevoir des méthodes permettant d’améliorer l’interopérabilité sémantique des systèmes CAO moyennant les technologies du Web Sémantique comme les ontologies OWL DL et le langage des règles SWRL. Nous avons donc élaboré une approche d’échange basée sur une ontologie commune de features de conception, que nous avons appelée CDFO « Common Design Features Ontology », servant d’intermédiaire entre les différents systèmes CAO. Cette approche s’appuie principalement sur deux grandes étapes. La première étape consiste en une homogénéisation des formats de représentation des modèles CAO vers un format pivot, en l’occurrence OWL DL. Cette homogénéisation sert à traiter les hétérogénéités syntaxiques entre les formats des modèles. La deuxième étape consiste à définir des règles permettant la mise en correspondance sémantique entre les ontologies d’application de CAO et notre ontologie commune. Cette méthode de mise en correspondance se base principalement, d’une part, sur la définition explicite des axiomes et des règles de correspondance permettant l’alignement des entités de différentes ontologies, et d’autre part sur la reconnaissance automatique des correspondances sémantiques supplémentaires à l’aide des capacités de raisonnement fournies par les moteurs d’inférence basés sur les logiques de description. Enfin, notre méthode de mise en correspondance est enrichie par le développement d’une méthode de calcul de similarité sémantique appropriée pour le langage OWL DL, qui repose principalement sur les composants des entités en question tels que leur description et leur contexte. / A major issue in product development is the exchange and sharing of product knowledge among many actors. This knowledge includes many concepts such as design history, component structure, features, parameters, constraints, and more. Heterogeneous tools and multiple designers are frequently involved in collaborative product development, and designers often use their own terms and definitions to represent a product design. Thus, to efficiently share design information among multiple designers, the design intent should be persistently captured and the semantics of the modeling terms should be semantically processed both by design collaborators and intelligent systems. Regarding CAD models, most of the current CAD systems provide feature-based design for the construction of solid models. Features are devised to carry, semantically, product information throughout its life cycle. Consequently, features should be maintained in a CAD model during its migration among different applications. However, existing solutions for exchanging product information are limited to the process of geometrical data, where semantics assigned to product model are completely lost during the translation process. Current standards, such as ISO 10303, known as STEP have attempted to solve this problem, but they define only syntactic data representation so that semantic data integration is not possible. Moreover, STEP does not provide a sound basis to reason with knowledge. Our research investigates the use of Semantic Web technologies, such as ontologies and rule languages; e.g. SWRL, for the exchange of “intelligent” CAD models among different systems, while maintaining the original relations among entities of the model. Thus, we have proposed an ontological approach based on the construction of a common design features ontology, used as an Interlingua for the exchange of product data. This ontology is represented formally with OWL DL. Furthermore, axioms and mapping rules are defined to achieve the semantic integration between the applications ontologies and the common ontology. The integration process relies basically on reasoning capabilities provided by description logics in order to recognize automatically additional mappings among ontologies entities. Furthermore, the mapping process is enhanced with a semantic similarity measure in order to detect similar design features. However, this will enable data analysis, as well as manage and discover implicit relationships among product data based on semantic modeling and reasoning.

A Web Semântica é uma maneira de explorar a associação de significados explícitos aos conteúdos de documentos presentes na Web, para que esses possam ser processados diretamente ou indiretamente por máquinas. Para possibilitar esse processamento, os computadores necessitam ter acesso a coleções estruturadas de informações e a conjuntos de regras de inferência sobre esses conteúdos. O SWRL permite a combinação de regras e termos de ontologias (definidos por OWL) para aumentar a expressividade de ambos. Entretanto, conforme um conjunto de regras cresce, ele torna-se de difícil compreensão e sujeito a erros, especialmente quando mantido por mais de uma pessoa. Para que o SWRL se torne um verdadeiro padrão web, deverá ter a capacidade de lidar com grandes conjuntos de regras. Para encontrar soluções para este problema, primeiramente, foi realizado um levantamento sobre sistemas de regras de negócios, descobrindo os principais recursos e interfaces utilizados por eles, e então, com as descobertas, propusemos técnicas que usam novas representações visuais em uma aplicação web. Elas permitem detecção de erro, identificação de regras similares, agrupamento, visualização de regras e o reuso de átomos para novas regras. Estas técnicas estão implementadas no SWRL Editor, um plug-in open-source para o Web-Protégé (um editor de ontologias baseado na web) que utiliza ferramentas de colaboração para permitir que grupos de usuários possam não só ver e editar regras, mas também comentar e discutir sobre elas. Foram realizadas duas avaliações do SWRL Editor. A primeira avaliação foi um estudo de caso para duas ontologias da área biomédica (uma área onde regras SWRL são muito usadas) e a segunda uma comparação com os únicos três editores de regras SWRL encontrados na literatura. Nessa comparação foi mostrando que ele implementa mais recursos encontrados em sistemas de regras em geral / The Semantic Web is a way to associate explicitly meaning to the content of web documents to allow them to be processed directly by machines. To allow this processing, computers need to have access to structured collections of information and sets of rules to reason about these content. The Semantic Web Rule Language (SWRL) allows the combination of rules and ontology terms, defined using the Web Ontology Language (OWL), to increase the expressiveness of both. However, as rule sets grow, they become difficult to understand and error prone, especially when used and maintained by more than one person. If SWRL is to become a true web standard, it has to be able to handle big rule sets. To find answers to this problem, we first surveyed business rule systems and found the key features and interfaces they used and then, based on our finds, we proposed techniques and tools that use new visual representations to edit rules in a web application. They allow error detection, rule similarity analysis, rule clustering visualization and atom reuse between rules. These tools are implemented in the SWRL Editor, an open source plug-in for Web-Protégé (a web-based ontology editor) that leverages Web-Protégés collaborative tools to allow groups of users to not only view and edit rules but also comment and discuss about them. We have done two evaluations of the SWRL Editor. The first one was a case study of two ontologies from the biomedical domain, the second was a comparison with the SWRL editors available in the literature, there are only three. In this comparison, it has been shown that the SWRL Editor implements more of the key resources found on general rule systems than the other three editors

A Web Semântica é uma maneira de explorar a associação de significados explícitos aos conteúdos de documentos presentes na Web, para que esses possam ser processados diretamente ou indiretamente por máquinas. Para possibilitar esse processamento, os computadores necessitam ter acesso a coleções estruturadas de informações e a conjuntos de regras de inferência sobre esses conteúdos. O SWRL permite a combinação de regras e termos de ontologias (definidos por OWL) para aumentar a expressividade de ambos. Entretanto, conforme um conjunto de regras cresce, ele torna-se de difícil compreensão e sujeito a erros, especialmente quando mantido por mais de uma pessoa. Para que o SWRL se torne um verdadeiro padrão web, deverá ter a capacidade de lidar com grandes conjuntos de regras. Para encontrar soluções para este problema, primeiramente, foi realizado um levantamento sobre sistemas de regras de negócios, descobrindo os principais recursos e interfaces utilizados por eles, e então, com as descobertas, propusemos técnicas que usam novas representações visuais em uma aplicação web. Elas permitem detecção de erro, identificação de regras similares, agrupamento, visualização de regras e o reuso de átomos para novas regras. Estas técnicas estão implementadas no SWRL Editor, um plug-in open-source para o Web-Protégé (um editor de ontologias baseado na web) que utiliza ferramentas de colaboração para permitir que grupos de usuários possam não só ver e editar regras, mas também comentar e discutir sobre elas. Foram realizadas duas avaliações do SWRL Editor. A primeira avaliação foi um estudo de caso para duas ontologias da área biomédica (uma área onde regras SWRL são muito usadas) e a segunda uma comparação com os únicos três editores de regras SWRL encontrados na literatura. Nessa comparação foi mostrando que ele implementa mais recursos encontrados em sistemas de regras em geral / The Semantic Web is a way to associate explicitly meaning to the content of web documents to allow them to be processed directly by machines. To allow this processing, computers need to have access to structured collections of information and sets of rules to reason about these content. The Semantic Web Rule Language (SWRL) allows the combination of rules and ontology terms, defined using the Web Ontology Language (OWL), to increase the expressiveness of both. However, as rule sets grow, they become difficult to understand and error prone, especially when used and maintained by more than one person. If SWRL is to become a true web standard, it has to be able to handle big rule sets. To find answers to this problem, we first surveyed business rule systems and found the key features and interfaces they used and then, based on our finds, we proposed techniques and tools that use new visual representations to edit rules in a web application. They allow error detection, rule similarity analysis, rule clustering visualization and atom reuse between rules. These tools are implemented in the SWRL Editor, an open source plug-in for Web-Protégé (a web-based ontology editor) that leverages Web-Protégés collaborative tools to allow groups of users to not only view and edit rules but also comment and discuss about them. We have done two evaluations of the SWRL Editor. The first one was a case study of two ontologies from the biomedical domain, the second was a comparison with the SWRL editors available in the literature, there are only three. In this comparison, it has been shown that the SWRL Editor implements more of the key resources found on general rule systems than the other three editors