Anotações têm sido associadas a documentos em todas as gerações de sistemas hipermídia. Este trabalho explora o uso de anotações como hiperdocumentos de primeira classe baseados em sua semântica. Nesse contexto, anotações são entidades próprias, na forma de hipertexto, possuindo seus próprios atributos e operações. A Web Semântica é uma extensão da Web atual na qual é dado um significado bem definido à informação, permitindo que informações sejam compreensíveis não só por humanos, mas também por computadores. Este trabalho possui como objetivo prover um serviço aberto, o GroupNote, de suporte a anotações colaborativas como hiperdocumentos de primeira classe na Web Semântica. Para prover esse serviço foram realizadas a modelagem conceitual e a definição e implementação de uma API, a API GroupNote. Como um estudo de caso do serviço GroupNote foi construída a aplicação WebNote, uma ferramenta que permite que usuários tenham seu próprio repositório de anotações na Web. / Annotations have been associated with documents in all the generations of hypermedia systems. This work investigates annotations as first class hyperdocuments based on their semantics: annotations are entities (with their own attributes and operations) in the hypertext form. The Semantic Web is an extension of the current Web in which a well-defined meaning is given to information, allowing the information to be comprehensible not only by humans, but also by machines. This work aims at providing an open service, GroupNote, to support collaborative annotations as first class hyperdocuments in the Semantic Web. The provision of the GroupNote service demanded the conceptual modeling, the definition and implementation of its API. As a case study of the GroupNote service, the WebNote application was built as a tool that allows users to have your own repository of annotations in the Web.

Cette thèse rentre dans le cadre du projet MEAT (Mémoire d´Expériences pour l´Analyse du Transcriptome) dont le but est d´assister les biologistes travaillant dans le domaine des puces à ADN, pour l´interprétation et la validation de leurs résultats. Nous proposons une aide méthodologique et logicielle pour construire une mémoire d´expériences pour ce domaine. Notre approche, basée sur les technologies du web sémantique, repose sur l´utilisation des ontologies et des annotations sémantiques sur des articles scientifiques et d´autres sources de connaissances du domaine. Dans une première partie, nous proposons une ontologie modulaire pour la description des connaissances du domaine des puces à ADN (base de données d´expériences, articles scientifiques, entités biomédicales...). Cette ontologie intègre entre autres, le réseau sémantique déjà existant d´UMLS, ce qui nous a permis d´approfondir le problème de réutilisation de ressources termino-ontologiques et leur adaptation à une nouvelle application. Ensuite, nous proposons une méthodologie générique pour la génération d´annotations sémantiques basées sur cette ontologie en exploitant les connaissances contenues dans les textes. Cette méthodologie a l´originalité d´utiliser des techniques de traitement automatique de la langue et des grammaires d´extraction de relations pour extraire automatiquement des articles scientifiques les relations reliant des termes d´UMLS reconnus dans le texte. Un système supportant cette méthodologie a été implémenté et validé par nos collègues biologistes. Enfin, pour faciliter la diffusion des connaissances contenues dans la mémoire, nous proposons un prototype qui se base sur un moteur de recherche sémantique (Corese) et qui exploite la base d´annotations que nous avons constituée. Cette partie du travail a permis d´améliorer la tâche de recherche d´informations en la rendant plus efficace et en offrant des mécanismes de raisonnement sur les connaissances du domaine.

Ce manuscrit présente une réflexion sur la terminaison des systèmes de réécriture d'ordres supérieurs. Nous nous concentrons sur une méthode particulière, la terminaison à base de tailles. La terminaison à base de tailles utilise le typage pour donner une approximation syntaxique à la taille d'un élément du langage. Notre contribution est double: premièrement, nous permettons d'aborder de manière structurée le problème de la correction des approches à base de taille. Pour ce faire, nous montrons qu'elle peut être traitée par une version de la méthode des annotations sémantiques. Cette dernière utilise des annotations sur les termes calculés à partir de la sémantique des sous-termes dans un certain prémodèle équationnel. Nous montrons la correction de notre approche par annotations sémantiques, ainsi que du critère qui permet de traiter le système annoté, et nous construisons un prémodèle pour le système qui correspond intuitivement à la sémantique du système de réécriture. Nous montrons alors que le système annoté passe le critère de terminaison. D'un autre coté nous modifions l'approche classique de la terminaison à base de tailles et montrons que le système modifié permet une analyse fine du flot de contrôle dans un langage d'ordre supérieur. Ceci nous permet de construire un graphe, dit graphe de dépendance approximé, et nous pouvons montrer qu'un critère syntaxique sur ce graphe suffit à montrer la terminaison de tout terme bien typé.

M.S. / Computer Science and Engineering / Genome-wide studies are sensitive to the quality of annotation data included for analyses and they often involve overlaying both computationally derived and experimentally generated data onto a genomic scaffold. A framework for successful integration of data from diverse sources needs to address, at a minimum, the conceptualization of the biological identity in the data sources, the relationship between the sources in terms of the data present, the independence of the sources and, any discrepancies in the data. The outcome of the process should either resolve or incorporate these discrepancies into downstream analyses. In this thesis we identify factors that are important in detecting errors within and between sources and present a generalized framework to detect discrepancies. An implementation of our workflow is used to demonstrate the utility of the approach in the construction of a genome-wide mouse transcription factor binding map and in the classification of Single nucleotide polymorphisms. We also present the impact of these discrepancies on downstream analyses. The framework is extensible and we discuss future directions including summarization of the discrepancies in a biological relevant manner.

<p>This study has been carried out as a part of the EC funded project, SMARTDOC IST-2000-28137, with the objective of developing application components that provide highly interactive visualization and collaboration functionalities. The low-level components from the graphics library AVS OpenViz 2.0 are used as the development basis. The application components can be inserted into electronic documents that allow embedded controls such as web documents or Microsoft Word or PowerPoint documents. Instead of displaying results as static images, a SMARTDOC component provides the ability to visualize data and interact with it inside the document. </p><p>Although the principal goal of the SMARTDOC project is to create components in a number of different application domains this study concentrates on developing a medical imaging application component in collaboration with the project partners AETmed and professor Alan Jackson at the University of Manchester. By incorporating the application component into patient reports, the clinicians are provided the ability to interact with the 3D data that is described in the reports. To improve the usability of the component, it makes use of a visual user interface (VUI), which gives the user the ability to interact and change parameters directly in the visualization process. </p><p>Collaborative work over geographical distances is an area that is becoming increasingly common and thus more interesting. As the availability of bandwidth has increased and the communication technologies have advanced, many companies express their interest for this new practical method of work. A company with offices in different countries would benefit from collaborative techniques providing closer cooperation within the company. Specialized institutions and laboratories could gather much experience and information through collaborative research. Medical imaging and visualization technique are areas where distinct disciplines such as networking, user interfaces and 3D visualization naturally can be fused together in order to develop collaborative environments. The visualization components developed within the SMARTDOC project will be the foundation for collaborative application components integrated with the Microsoft DirectX^® multimedia library. In the medical imaging area, collaborative work can be used to improve diagnoses, journaling and teaching. </p><p>This study focuses on developing a prototype of an interactive visualization component for 3D medical imaging and creating a collaborative environment using a multimedia library originally meant for network gaming.</p>

Ce mémoire traite de la question des annotations en environnement virtuel pour aider à la conception collaborative de produit. Pour ceci, nous nous inspirons de deux approches : d'une part l'utilisation de la réalité virtuelle pour la conception collaborative, et d'autre part la gestion des connaissances.<br />Notre premier apport est la définition d'un modèle de l'annotation 3D, qui comporte trois parties : la forme, la spatialisation et les méta-données. Nous présentons en particulier les supports spécifiques de l'annotation 3D, l'ancre et le point de vue géométrique.<br />Nous proposons, afin de gérer le grand nombre d'annotations et l'absence d'ordre canonique de lecture d'un objet 3D, l'introduction d'une ontologie indexant les annotations.<br />A l'aide de notre environnement prototype, nous avons évalué l'influence de l'utilisation de l'ontologie sur la lecture des annotations 3D. Les résultats indiquent un apport de l'ontologie, les utilisateurs trouvant plus facilement l'information pertinente.

Cys2-His2 (C2H2) zinc finger domains were originally identified as DNA binding domains, and uncharacterized domains are typically assumed to bind DNA. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. Over 100 C2H2 zinc finger-protein interactions have been described. This study uses common bioinformatics tools to identify sequence features that predict a DNA- or protein-binding function. Several issues, including uncertainties about the full functional capabilities of the zinc fingers, complicated these efforts. Therefore, an unbiased approach which directly examined the potential for zinc fingers to facilitate DNA or protein interactions was used to determine the full functional capabilities of the C2H2 domains in two model proteins, human OLF-1/EBF associated zinc finger (OAZ) protein and Zif268. OAZ contains 30 zinc fingers in six clusters, some of which have been previously indicated in DNA or protein interactions. Zif268 is a well-known DNA binding protein with three C2H2 domains. DNA binding was assessed using a target site selection (CAST) assay, and protein binding was assessed using a yeast two-hybrid assay. Results indicate that clusters known to bind DNA could facilitate specific protein interactions, but clusters known to bind protein did not facilitate specific DNA interactions, indicating that DNA binding is a more restricted function of zinc fingers than has previously been recognized. These results also suggest that the role of C2H2 zinc finger domains in protein interactions has probably been underestimated. The implication of these findings for the prediction of zinc finger function is discussed.

Software development requires understanding and navigating complex software spaces. Developers frequently utilize annotations in source code to help them externalize information they need to remember, such as tasks and implementation details. Although some tool support exists in modern integrated development environments for authoring and navigating these annotations, we have observed that they often fail to remind developers about tasks that need to be performed and are sometimes difficult to find. We present the results from four empirical studies designed to better understand how developers create and manage their information using annotations. We also explore the use of hierarchical tagging capabilities to enhance these annotations. Based on the findings from these studies, we provide suggestions on how annotation tools may be improved.

Software development requires understanding and navigating complex software spaces. Developers frequently utilize annotations in source code to help them externalize information they need to remember, such as tasks and implementation details. Although some tool support exists in modern integrated development environments for authoring and navigating these annotations, we have observed that they often fail to remind developers about tasks that need to be performed and are sometimes difficult to find. We present the results from four empirical studies designed to better understand how developers create and manage their information using annotations. We also explore the use of hierarchical tagging capabilities to enhance these annotations. Based on the findings from these studies, we provide suggestions on how annotation tools may be improved.

The Internet as we know it today has sustained continuous evolution since its creation, radically changing means of communication and ways in which commerce is globally operated. From the World Wide Web to the two-way video calls, it has shifted the ways people communicate and societies function. The Internet itself was first conceived as a network that would enable the communication between multiple trusted and known hosts, but as the time passed, it has notably evolved. Due to the significant adoption of Internet-connected devices (phones, personal computers, tablets...), the initial device homogeneity has shifted towards an extremely heterogeneous environment in which many different devices consume and publish resources, also referred as services. As the number of connected devices and resources increases, it becomes critical to building systems that enable the autonomic publication, consumption, and retrieval of those resources. As the inherent complexity of systems continues to grow, it is essential to set boundaries to their achievable capabilities. The traditional approaches to network-based computing are not sufficient, and new reference approaches should be presented. In this context the Future Internet (FI) term emerges, a worldwide execution environment connecting large sets of heterogeneous and autonomic devices and resources. In such environments, systems leverage service annotations to fulfil emerging goals and dynamically organise resources based on interests. Although research has been conducted in those areas, active research is being carried out in the following areas: extensible machine-readable annotation of services, dynamic service discovery, architectural approaches for decentralised systems, and interest-focused dynamic service organisations. These concepts will be explained in the next section, as they will serve to contextualise the later presented problem statement and research questions.