A representação e execução de processos de negócio têm gerado importantes desafios na área de Ciência da Computação. Um desses desafios é a escolha do melhor arcabouço formal para a especificação dos controles de fluxo padrões. Algumas linguagens defendem o uso de redes de Petri ou álgebras de processos como base formal. O uso de redes de Petri para especificar workflows clássicos é uma abordagem bastante conhecida. Entretanto, pesquisas recentes vêm difundindo o uso de novas extensões da álgebra de processos como uma alternativa para a especificação formal de workflows. A principal contribuição deste trabalho é a definição da Navigation Plan Definition Language (NPDL). A NPDL foi implementada como uma extensão da linguagem SQL. Ela é uma alternativa para a representação de workflows que utiliza a álgebra de processos como arcabouço formal. A NPDL promove uma separação explícita entre o ambiente de especificação e o ambiente de execução de um workflow. Esta separação propicia o reaproveitamento de passos de negócio e o uso das propriedades da álgebra de processos não só na modelagem, mas também no controle da execução dos processos. Após a especificação de um workflow por meio da NPDL, a execução dos passos que o definem é controlada pela ferramenta NavigationPlanTool. Essa ferramenta é a segunda contribuição deste trabalho de pesquisa. / The representation and execution of business processes have generated some important challenges in Computer Science. An important related concern is the choosing of the best formal foundation to represent control-flow patterns. Some of the workflow languages advocate the Petri nets or process algebra as formal foundation. The use of Petri nets is a famous approach to support classic workflows. On the other hand some researches are introducing modern process algebra extensions as an alternative formal foundation for representing workflows. The first contribution of this research is the definition of the Navigation Plan Definition Language (NPDL). NPDL was implemented as an extension of SQL language. It is an alternative to represent business processes using process algebra as formal foundation. NPDL provides the explicit separation between specification and execution workflow environment. This separation allows reusing of business steps and usage of process algebra properties in the process modeling and execution controlling tasks. After the definition of a workflow using NPDL, the business steps execution is carried out and controlled by a tool called NavigationPlanTool. This tool is the second contribution of this research.

Cada subtipo de HIV-1 tem um padrão mutacional próprio. Dados sobre mutações de resistência aos antiretrovirais foram obtidos com o subtipo B, primeiro em prevalência no Brasil. O segundo em algumas regiões é o subtipo F. Foram analisados padrões mutacionais em seqüências brasileiras de protease do subtipo F e levantou as seqüências deste subtipo disponíveis na base de dados de Stanford. A análise de dois grupos de seqüências (pacientes não tratados e tratados com inibidores de protease) mostrou 19 mutações associadas ao tratamento comuns ao subtipo B e 17 duplas de mutações associadas ao tratamento que diferem das descritas para o subtipo B, indicando a necessidade de estudos sobre rotas mutacionais no subtipo F. / Each HIV-1 subtype has a specific mutation pattern. Data on HIV-1 antiretroviral resistance mutations were obtained with subtype B, the first in prevalence in Brazil. The second in some regions is subtype F. Mutation patterns of Brazilian subtype F protease sequences were analyzed and performed a research of the sequences of Stanford Database. The analysis of two groups of sequences (untreated and treated patients with protease inhibitors) showed 19 treatment associated mutations also common in subtype B and 17 combinations of statistically treatment associated mutations that were quite different to those described for subtype B, indicating the need of studies to evaluate specific mutation pathways of subtype F.

Os sistemas de aplicações científicas e comerciais geram, cada vez mais, imensas quantidades de dados os quais dificilmente podem ser analisados sem que sejam usados técnicas e ferramentas adequadas de análise. Além disso, muitas destas aplicações são voltadas para Internet, ou seja, possuem seus dados distribuídos, o que dificulta ainda mais a realização de tarefas como a coleta de dados. A área de Extração de Conhecimento de Base de Dados diz respeito às técnicas e ferramentas usadas para descobrir automaticamente conhecimento embutido nos dados. Num ambiente de rede de computadores, é mais complicado realizar algumas das etapas do processo de KDD, como a coleta e processamento de dados. Dessa forma, pode ser feita a utilização de novas tecnologias na tentativa de auxiliar a execução do processo de descoberta de conhecimento. Os agentes de software são programas de computadores com propriedades, como, autonomia, reatividade e mobilidade, que podem ser utilizados para esta finalidade. Neste sentido, o objetivo deste trabalho é apresentar a proposta de um sistema multi-agente, chamado Minador, para auxiliar na execução e gerenciamento do processo de Extração de Conhecimento de Base de Dados. / Nowadays, commercial and scientific application systems generate huge amounts of data that cannot be easily analyzed without the use of appropriate tools and techniques. A great number of these applications are also based on the Internet which makes it even more difficult to collect data, for instance. The field of Computer Science called Knowledge Discovery in Databases deals with issues of the use and creation of the tools and techniques that allow for the automatic discovery of knowledge from data. Applying these techniques in an Internet environment can be particulary difficult. Thus, new techniques need to be used in order to aid the knowledge discovery process. Software agents are computer programs with properties such as autonomy, reactivity and mobility that can be used in this way. In this context, this work has the main goal of presenting the proposal of a multiagent system, called Minador, aimed at supporting the execution and management of the Knowledge Discovery in Databases process.

Com o intuito de tornarem-se mais eficientes, muitas organizações -- empresas, órgãos governamentais, centros de pesquisa, etc. -- optam pela utilização de ferramentas de software para apoiar a realização de seus processos. Uma opção que vem se tornando cada vez mais popular é a utilização de sistemas de Gestão de Processos de Negócio (GPN), que são ferramentas genéricas, ou seja, não são específicas a nenhuma organização, altamente configuráveis e ajustáveis às necessidades dos objetos de atuação de cada organização. Uma das principais responsabilidades de um sistema de GPN é prover mecanismos de tratamento de exceções à execução de instâncias de processos de negócio. Exceções, se forem ignoradas ou se não forem corretamente tratadas, podem causar o aborto da execução de instâncias e, dependendo da gravidade da situação, podem causar falhas em sistemas de GPN ou até mesmo em sistemas subjacentes (sistema operacional, sistema gerenciador de banco de dados, etc.). Sendo assim, mecanismos de tratamento de exceções têm por objetivo resolver a situação excepcional ou conter seus efeitos colaterais garantindo, ao menos, uma degradação controlada (graceful degradation) do sistema. Neste trabalho, estudamos algumas das principais deficiências de modelos atuais de tratamento de exceções, no contexto de sistemas de GPN, e apresentamos soluções baseadas em Modelos Transacionais Avançados para contorná-las. Isso é feito por meio do aprimoramento dos mecanismos de tratamento de exceções da abordagem de modelagem e gerenciamento de execução de processos de negócio WED-flow. Por fim, estendemos a ferramenta WED-tool, uma implementação da abordagem WED-flow, através do desenvolvimento de seu gerenciador de recuperação de falhas. / With the aim of becoming more efficient, many organizations -- companies, governmental entities, research centers, etc -- choose to use software tools for supporting the accomplishment of its processes. An option that becomes more popular is the usage of Business Process Management Systems (BPM), which are generic tools, that is, not specific to any organization and highly configurable to the domain needs of any organization. One of the main responsibilities of BPM Systems is to provide exception handling mechanisms for the execution of business process instances. Exceptions, if ignored or incorrectly handled, may induce the abortion of instance executions and, depending on the gravity of the situation, induce failures on BPM Systems or even on subjacent systems (operational system, database management systems, etc.). Thus, exception handling mechanisms aim to solve the exceptional situation or stopping its collateral effects by ensuring, at least, a graceful degradation to the system. In this work, we study some of the main deficiencies of present exception handling models -- in the context of BPM Systems -- and present solutions based on Advanced Transaction Models to bypass them. We do this through the improvement of exception handling mechanisms from WED-flow, a business process modelling and instance execution managing approach. Lastly, we extend the WED-tool, an implementation of WED-flow approach, through the development of its failure recovery manager.

Diferentes organizações dentro de um mesmo domínio de aplicação costumam ter requisitos de dados bastante semelhantes. Apesar disso, cada organização também tem necessidades específicas, que precisam ser consideradas no projeto e desenvolvimento dos sistemas de bancos de dados para o domínio em questão. Dessas necessidades específicas, resultam variações estruturais nos dados das organizações de um mesmo domínio. As técnicas tradicionais de modelagem conceitual de banco de dados (como o Modelo Entidade-Relacionamento - MER - e a Linguagem Unificada de Modelagem - UML) não nos permitem expressar em um único esquema de dados essa variabilidade. Para abordar esse problema, este trabalho de mestrado propôs um novo método de modelagem conceitual baseado no uso de Diagramas de Características de Banco de Dados (DBFDs, do inglês Database Feature Diagrams). Esse método foi projetado para apoiar a criação de famílias de esquemas conceituais de banco de dados. Uma família de esquemas conceituais de banco de dados compreende todas as possíveis variações de esquemas conceituais de banco de dados para um determinado domínio de aplicação. Os DBFDs são uma extensão do conceito de Diagrama de Características, usado na Engenharia de Linhas de Produtos de Software. Por meio dos DBFDs, é possível gerar esquemas conceituais de banco de dados personalizados para atender às necessidades específicas de usuários ou organizações, ao mesmo tempo que se garante uma padronização no tratamento dos requisitos de dados de um domínio de aplicação. No trabalho, também foi desenvolvida uma ferramenta Web chamada DBFD Creator, para facilitar o uso do novo método de modelagem e a criação dos DBFDs. Para avaliar o método proposto neste trabalho, foi desenvolvido um estudo de caso no domínio de dados experimentais de neurociência. Por meio do estudo de caso, foi possível concluir que o método proposto é viável para modelar a variabilidade de dados de um domínio de aplicação real. Além disso, foi realizado um estudo exploratório com um grupo de pessoas que receberam treinamentos, executaram tarefas e preencheram questionários de avaliação sobre o método de modelagem e a sua ferramenta de software de apoio. Os resultados desse estudo exploratório mostraram que o método proposto é reprodutível e que a ferramenta de software tem boa usabilidade, amparando de forma apropriada a execução do passo-a-passo do método. / Different organizations within the same application domain usually have very similar data requirements. Nevertheless, each organization also has specific needs that should be considered in the design and development of database systems for that domain. These specific needs result in structural variations in data from organizations of the same domain. The traditional techniques of database conceptual modeling (such as Entity Relationship Model - ERM - and Unified Modeling Language - UML) do not allow to express this variability in a single data schema. To address this problem, this work proposes a new conceptual modeling method based on the use of Database Feature Diagrams (DBFDs). This method was designed to support the creation of families of conceptual database schemas. A family of conceptual database schemas includes all possible variations of database conceptual schemas for a particular application domain. The DBFDs are an extension of the concept of Features Diagram used in the Software Product Lines Engineering. Through DBFDs, it is possible to generate customized database conceptual schemas to address the specific needs of users or organizations at the same time we ensure a standardized treatment of the data requirements of an application domain. At this work, a Web tool called DBFD Creator was also developed to facilitate the use of the new modeling method and the creation of DBFDs. To evaluate the method proposed in this work, a case study was developed on the domain of neuroscience experimental data. Through the case study, it was possible to conclude that the proposed method is feasible to model data variability of a real application domain. In addition, an exploratory study was conducted with a group of people who have received training, executed tasks and filled out evaluation questionnaires about the modeling method and its supporting software tool. The results of this exploratory study showed that the proposed method is reproducible and that the software tool has good usability, properly supporting the execution of the method\'s step-by-step procedure.

Die Bedeutung der in den relationalen Datenbankmanagementsystemen dargestellten Realwelt-Objekten wird weder explizit noch vollständig beschrieben. Demzufolge treffen häufig diese Systeme mit den Anfrageantworten nicht die Benutzerabsichten. Die vorliegende Dissertation präsentiert einen ontologie-basierten Ansatz für die semantische Anfrageverarbeitung. In diesem Ansatz sollen semantische Informationen aus einer gegebenen Ontologie abgeleitet und für die Umformulierung der Benutzeranfrage verwendet werden. Dies führt zu einer neuen Anfrage, die für den Benutzer sinnvollere Ergebnisse aus der Datenbank zurückliefern kann. Wir definieren und spezifizieren Einschränkungen und Abbildungen zwischen der Ontologie- und den Datenbank-Konzepten, um eine Ontologie mit einer Datenbank zu verknüpfen. Des Weiteren entwickeln wir eine Reihe von Algorithmen, die uns helfen, diese Abbildungen auf eine halbautomatische Weise zu finden. Au"serdem entwickeln wir eine Reihe von semantischen Regeln, die für die Umformulierung einer Anfrage benutzt werden. Die Haupteigenschaft einer Regel ist es, Begriffe einer Anfrage durch andere Begriffe zu ersetzen oder anzureichern, die von denselben ontologischen Konzepten dargestellt werden. Weiterhin benutzen wir die Theorie der Termersetzungssysteme, um den Transformationsprozess zu formalisieren und die wesentlichen Eigenschaften für das Anwenden der Regeln zu studieren. Aufbauend auf diesem Ansatz wurde ein Prototyp implementiert und wurde die Fähigkeit unseres Ansatzes durch einer real existierenden Anwendung ausgewertet. / Currently, database management systems solely rely on exact syntax of queries to retrieve data. As consequence query answers often do not meet the user''s intention. In this thesis we propose an ontology-based semantic query processing approach for database systems. We use ontologies to transform a user query into another query that may provide a more meaningful answer to the user. For this purpose, we define and specify different mappings that relate concepts of an ontology with those of an underlying database and develop a set of algorithms that allow us to find these mappings in a semi-automatic way. Moreover, we propose a set of semantic rules for transforming queries using terms derived from the ontology. We classify the rules and demonstrate their usefulness using practical examples. Furthermore, we make use of the theory of term rewriting systems to formalize the transformation process and to study the basic properties for applying these rules. Finally, we implement a prototype system using current technologies and evaluate its capability by using a real world application.

Dans cette thèse, nous nous intéressons à des problèmes à la croisée de deux domaines, les bases de données et les bases de connaissances. Nous considérons deux problèmes équivalents concernant les requêtes conjonctives avec négation : l'inclusion de requêtes et l'évaluation d'une requête booléenne sous l'hypothèse du monde ouvert. Nous reformulons ces problèmes sous la forme d'un problème de déduction dans un fragment de la logique du premier ordre. Puis nous raffinons des schémas d'algorithmes déjà existants et proposons de nouveaux algorithmes. Pour les étudier et les comparer expérimentalement, nous proposons un générateur aléatoire et analysons l'influence des différents paramètres sur la difficulté des instances du problème étudié. Finalement, à l'aide de cette méthodologie expérimentale, nous comparons les apports des différents raffinements et les algorithmes entre eux. / In this thesis, we consider problems at the intersection of two areas: databases and knowledge bases. We focus on two equivalent problems on conjunctive queries with negation : query containment and query answering with boolean queries while making the open-world assumption. We reformulate these problems as a problem of deduction in a first order logic fragment. Then we refine existing algorithm schemes and propose new algorithms. To study and compare them experimentally, we propose a random generator and we analyze the influence of parameters on problem instances difficulty. Finally, we analyse the contributions of the different refinements and we compare experimentally the algorithms.

Les motifs graduels visent à décrire des co-variations au sein des données et sont de la forme plus l'âge est important, plus le salaire est élevé. Ces motifs ont fait l'objet de nombreux travaux en fouille de données ces dernières années, du point de vue des définitions que peuvent avoir de tels motifs et d'un point de vue algorithmique pour les extraire efficacement. Ces définitions et algorithmes considèrent qu'il est possible d'ordonner de manière stricte les valeurs (par exemple l'âge, le salaire). Or, dans de nombreux champs applicatifs, il est difficile voire impossible d'ordonner de cette manière. Par exemple, quand l'on considère l'expression de gènes, dire que l'expression d'un gène est plus importante que l'expression d'un autre gène quand leurs expressions ne diffèrent qu'à la dixième décimale n'a pas de sens d'un point de vue biologique. Ainsi, nous proposons dans cette thèse une approche fondée sur les ordres flous. Les algorithmes étant très consommateurs tant en mémoire qu'en temps de calcul, nous proposons des optimisations d'une part du stockage des degrés flous et d'autre part de calcul parallélisé. Les expérimentations que nous avons menées sur des bases de données synthétiques et réelles montrent l'intérêt de notre approche. / Gradual patterns aim at describing co-variations of data such as the older, the higher the salary. They have been more and more studied from the data mining point of view in recent years, leading to several ways of defining their meaning and and several algorithms to automatically extract them.They consider that data can be ordered regarding the values taken on the attributes (e.g. the age and the salary).However, in many application domains, it is hardly possible to consider that data values are crisply ordered. For instance, when considering gene expression, it is not true, from the biological point of view, to say that Gene 1 is more expressed than Gene 2 if the levels of expression only differ from the tenth decimal. This thesis thus considers fuzzy orderings and propose both formal definitions and algorithms to extract gradual patterns considering fuzzy orderings. As these algorithms are both time and memory consuming, we propose some optimizations based on an efficient storage of the fuzzy ordering informationcoupled with parallel algorithms. Experimental results run on synthetic and real database show the interest or our proposal.

Au cours des dernières années, le volume des données qui sont capturées et générées a explosé. Les progrès des technologies informatiques, qui fournissent du stockage à bas prix et une très forte puissance de calcul, ont permis aux organisations d'exécuter des analyses complexes de leurs données et d'en extraire des connaissances précieuses. Cette tendance a été très importante non seulement pour l'industrie, mais a également pour la science, où les meilleures instruments et les simulations les plus complexes ont besoin d'une gestion efficace des quantités énormes de données.Le parallélisme est une technique fondamentale dans la gestion de données extrêmement volumineuses car il tire parti de l'utilisation simultanée de plusieurs ressources informatiques. Pour profiter du calcul parallèle, nous avons besoin de techniques de partitionnement de données efficaces, qui sont en charge de la division de l'ensemble des données en plusieurs partitions et leur attribution aux nœuds de calculs. Le partitionnement de données est un problème complexe, car il doit prendre en compte des questions différentes et souvent contradictoires telles que la localité des données, la répartition de charge et la maximisation du parallélisme.Dans cette thèse, nous étudions le problème de partitionnement de données, en particulier dans les bases de données parallèles scientifiques qui sont continuellement en croissance. Nous étudions également ces partitionnements dans le cadre MapReduce.Dans le premier cas, nous considérons le partitionnement de très grandes bases de données dans lesquelles des nouveaux éléments sont ajoutés en permanence, avec pour exemple une application aux données astronomiques. Les approches existantes sont limitées à cause de la complexité de la charge de travail et l'ajout en continu de nouvelles données limitent l'utilisation d'approches traditionnelles. Nous proposons deux algorithmes de partitionnement dynamique qui attribuent les nouvelles données aux partitions en utilisant une technique basée sur l'affinité. Nos algorithmes permettent d'obtenir de très bons partitionnements des données en un temps d'exécution réduit comparé aux approches traditionnelles.Nous étudions également comment améliorer la performance du framework MapReduce en utilisant des techniques de partitionnement de données. En particulier, nous sommes intéressés par le partitionnement efficient de données d'entrée / During the last years, the volume of data that is captured and generated has exploded. Advances in computer technologies, which provide cheap storage and increased computing capabilities, have allowed organizations to perform complex analysis on this data and to extract valuable knowledge from it. This trend has been very important not only for industry, but has also had a significant impact on science, where enhanced instruments and more complex simulations call for an efficient management of huge quantities of data.Parallel computing is a fundamental technique in the management of large quantities of data as it leverages on the concurrent utilization of multiple computing resources. To take advantage of parallel computing, we need efficient data partitioning techniques which are in charge of dividing the whole data and assigning the partitions to the processing nodes. Data partitioning is a complex problem, as it has to consider different and often contradicting issues, such as data locality, load balancing and maximizing parallelism.In this thesis, we study the problem of data partitioning, particularly in scientific parallel databases that are continuously growing and in the MapReduce framework.In the case of scientific databases, we consider data partitioning in very large databases in which new data is appended continuously to the database, e.g. astronomical applications. Existing approaches are limited since the complexity of the workload and continuous appends restrict the applicability of traditional approaches. We propose two partitioning algorithms that dynamically partition new data elements by a technique based on data affinity. Our algorithms enable us to obtain very good data partitions in a low execution time compared to traditional approaches.We also study how to improve the performance of MapReduce framework using data partitioning techniques. In particular, we are interested in efficient data partitioning of the input datasets to reduce the amount of data that has to be transferred in the shuffle phase. We design and implement a strategy which, by capturing the relationships between input tuples and intermediate keys, obtains an efficient partitioning that can be used to reduce significantly the MapReduce's communication overhead.

We survey and compare the different major mechanisms for embedding the relational database language SQL in object-oriented programming languages such as Java and C#, with regard to how much impedance mismatch these embeddings suffer. Here impedance mismatch refers to clarity and performance difficulties that arise because of the nature of the embedding. Because of the central position in the information technology industry of object-oriented programs that access SQL-based relational database systems, reducing impedance mismatch is generally recognized in that industry as an important practical problem. We argue for the suitability of SQL as a database language, and hence for the desirability of keeping SQL as the view provided by a SQL embedding. We make the case that SQLJ, a SQL embedding for Java in which it appears that Java directly supports SQL commands, is the kind of SQL embedding that suffers the least impedance mismatch, when compared with call-level interfaces and object-relational mappings. We propose extensions to SQLJ that would reduce its impedance mismatch even further. / by Jose Luis Hurtado. / Thesis (M.S.C.S.)--Florida Atlantic University, 2012. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.