Research of protein-protein interactions produce vast quantities of data and there exists a large number of databases with data from this research. Many of these databases offers the data for download on the web in a number of different formats, many of them XML-based. With the arrival of these XML-based formats, and especially the standardized formats such as PSI-MI, SBML and BioPAX, there is a need for searching in data represented in XML. We wanted to investigate the capabilities of XML query tools when it comes to searching in this data. Due to the large datasets we concentrated on native XML database systems that in addition to search in XML data also offers storage and indexing specially suited for XML documents. A number of queries were tested on data exported from the databases IntAct and Reactome using the XQuery language. There were both simple and advanced queries performed. The simpler queries consisted of queries such as listing information on a specified protein or counting the number of reactions. One central issue with protein-protein interactions is to find pathways, i.e. series of interconnected chemical reactions between proteins. This problem involve graph searches and since we suspected that the complex queries it required would be slow we also developed a C++ program using a graph toolkit. The simpler queries were performed relatively fast. Pathway searches in the native XML databases took long time even for short searches while the C++ program achieved much faster pathway searches.

Made available in DSpace on 2014-06-12T16:00:24Z (GMT). No. of bitstreams: 2 arquivo6556_1.pdf: 641759 bytes, checksum: 7046c38915c80e308e3cd3bc91890b55 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2007 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Sistemas de Integração de Dados (SID) proporcionam ao usuário uma visão unificada de dados que estão armazenados em diversas fontes diferentes. Essas fontes são independentes e cada uma possui um esquema próprio, elaborado para atender as necessidades dos usuários de cada banco. Cada SID possui um conjunto de fontes de dados distintas relevantes para o seu domínio, e deve colher de cada uma os dados necessários para responder as consultas do usuário. Uma vez obtidos esses dados, o SID deverá traduzi-los para um esquema global (esquema de mediação), integrá-los e exibi-los ao usuário. Para Sistemas de Integração de Dados na Web, como o Integra - SID desenvolvido por alunos e professores do Centro de Informática da UFPE e utilizado para a implementação das nossas contribuições - os desafios são ainda maiores, visto que a disponibilidade das fontes se torna um fator bastante relevante. Sendo assim, o custo para se buscar os dados sempre nas fontes pode ser bastante alto. Por isso, alguns SID, como o Integra, possuem uma cache para o armazenamento dos dados resultantes das consultas que o sistema considera mais relevantes. Desta forma, quando alguma consulta que já esteja armazenada em cache for novamente solicitada pelo usuário, o sistema não mais necessitará acessar as fontes de dados para respondê-la, o que otimizará o processamento. O objetivo desta dissertação de mestrado é apresentar uma proposta de um Gerenciador de Cache para um Sistema de Integração de Dados. Esse Gerenciador é composto por um módulo que controla o espaço da cache, decidindo que consultas devem entrar e quais devem permanecer em cache. Possui outro módulo que identifica se a consulta submetida pelo usuário está contida em outra que esteja armazenada em cache (técnica de query containment). E por último, um módulo que realiza a substituição parcial de uma consulta, para o melhor aproveitamento do espaço da cache

El almacenamiento digital de la información debe abordar tanto el problema de la incorporación de datos al sistema como su recuperación, y debe hacer un catálogo acorde con las consultas que sobre ellos quiera hacerse. El espacio ocupado para el almacenamiento y el tiempo necesario para ingresar la información, y para recuperala, depende directamente de la estructura utilizada en el repositorio. De este modo, cuando nos referimos a información que ya cuenta cion un grado de estructuración, la indexación debe ser coherente con la estructuta formal de la misma, para favorecer así la consulta. En el presente estudio se aborda el problema de la compresión estática de información semi-estructurada combinada con una indezación tendiente a soportar uin conjunto de consultas sobre los datos, con un fuerte énfasis en el almacenamiento en memoria secundaria. El ámbito de desarrollo de la aplicación propuesta se enmarca dentro de la documentación XML y su lenguaje de consulta XQuery. El modelo utilizado en la implementación está basado en la propuestas desarrolladas por Baeza-Yates y Navarro en Proximal Nodes. La implementación corresponde a un desarrollo posterior de un procesador destinado a soportar consultas en el lenguaje XPath desarrollado por Manuel Ortega como memoria de Ingeniería. El desarrollo de la capa de almacenamiento del prototipo actual se enfoca en la resolución de problemas en tres áreas: recuperación del archivo fuente, consulta eficiente sobre la estructura del documento, y búsqueda de texto en lenguaje natural. Las estructuras diseñadas adhieren a técnicas recientes en el área de la compresión y de recuperación de la información en XML. El resultado de esta memoria es un autoíndice XML con gran desempeño en colecciones de tamaño pequeño y mediano, con capacidad de abordar colecciones de gran tamaño con resucesos limitados de memoria principal, y con un gran potencial de adaptación para colecciones en un nuevo contexto dinámico. El prototipo presenta un desempeño altamente competitivo con las alternativas existentes en el estado del arte.

No description available.

Le langage XML est devenu un standard de représentation et d'échange de données à travers le web. Le but de la réplication de données au sein de différents sites est de minimiser le temps d'accès à ces données partagées. Cependant, différents problèmes sont liés à la sécurisation de ces données. Le but de cette thèse est de proposer des modèles de contrôles d'accès XML qui prennent en compte les droits de lecture et de mise-à-jour et qui permettent de surmonter les limites des modèles qui existent. Nous considérons les langages XPath et XQuery Update Facility pour la formalisation des requêtes d'accès et des requêtes de mise-à-jour respectivement. Nous donnons des descriptions formelles de nos modèles de contrôles d'accès et nous présentons des algorithmes efficaces pour le renforcement des politiques de sécurité spécifiées à la base de ces modèles. L'autre partie de cette thèse est consacrée à l'étude pratique de nos propositions. Nous présentons notre système appelé SVMAX qui met en oeuvre nos solutions, et nous conduisons une étude expérimentale basée sur une DTD réelle pour montrer son efficacité. Plusieurs systèmes de bases de données natives (systèmes de BDNs) ont été proposés récemment qui permettent une manipulation efficace des données XML en utilisant la plupart des standards du W3C. Nous montrons que notre système SVMAX peut être intégré facilement et efficacement au sein d'un large ensemble de systèmes de BDNs. A nos connaissances, SVMAX est le premier système qui permet la sécurisation des données XML conformes à des DTDs arbitraires (récursives ou non) et ceci en moyennant un fragment significatif de XPath et une classe riche d'opérations de mise-à-jour XML / XML has become a standard for representation and exchange of data across the web. Replication of data within different sites is used to increase the availability of data by minimizing the access's time to the shared data. However, the safety of the shared data remains an important issue. The aim of the thesis is to propose some models of XML access control that take into account both read and update rights and that overcome limitations of existing models. We consider the XPath language and the XQuery Update Facility to formalize respectively user access queries and user update operations. We give formal descriptions of our read and update access control models and we present efficient algorithms to enforce policies that can be specified using these models. Detailed proofs are given that show the correctness of our proposals. The last part of this thesis studies the practicality of our proposals. Firstly, we present our system, called SVMAX, that implements our solutions and we conduct an extensive experimental study, based on real-life DTD, to show that it scales well. Many native XML databases systems (NXD systems) have been proposed recently that are aware of the XML data structure and provide efficient manipulation of XML data by the use of most of W3C standards. Finally, we show that our system can be integrated easily and efficiently within a large set of NXD systems, namely BaseX, Sedna and eXist-db. To the best of our knowledge, SVMAX is the first system for securing XML data in the presence of arbitrary DTDs (recursive or not), a significant fragment of XPath and a rich class of XML update operations

XML is an emerging standard format for data on the Web as well as in business applications. In order to store and access this information in an efficient manner, database technology must be utilized. A relational database system, the most established and mature technology for query processing and storage, creates a strong foundation for such an XML data management system. However, while relational databases are based on SQL queries, the original user queries are written in XQuery, an XML query language. This XML query language has support for order-sensitive queries as XML is an order-sensitive markup language. A major problem has been discovered with loading XML in a relational database. That problem is the lack of native SQL support for and management of order handling. While XQuery has order and positional support, SQL does not have the same support. For example, individuals who were viewing XML information about music albums would have a hard time querying for the first three songs of a track list from a relational backend. Mapping XML documents to relational backends also proves hard as the data models (hierarchical elements versus flat tables) are so different. For these reasons, and other purposes, the Rainbow System is being developed at WPI as a system that bridges XML data and relational data. This thesis in particular deals with the algebra operators that affect order, order sensitive loading and mapping of XML documents, and the pushdown of order handling into SQL-capable query engines. The contributions of the thesis are the order-sensitive rewrite rules, new XML to relational mappings with different order styles, order-sensitive template-driven SQL generation, and a proposed metadata table for order-sensitive information. A system that implements these proposed techniques with XQuery as the XML query language and Oracle as the backend relational storage system has been developed. Experiments were created to measure execution time based on various factors. First, scalability of the system as backend data set size grows is studied. Second, scalability of the system as results returned from the database grows, and finally, query execution times with different loading types are explored. The experimental results are encouraging. Query execution with the relational backend proves to be much faster than native execution within the Rainbow system. These results confirm the practical utility of our proposed order-sensitive XQuery execution solution over relational data.

"XML Stream Processing is an emerging technology designed to support declarative queries over continuous streams of data. The interest in this novel technology is growing due to the increasing number of real world applications such as monitoring systems for stock, email, and sensor data that need to analyze incoming data streams. There are however several open challenges. One, we must develop efficient techniques for pattern matching over the nested tag structure of XML as data streams in token by token. Two, we must develop techniques for query optimization to cope with complex user queries while given only incomplete knowledge of source data. When considering these challenges separately, then automata models have been shown by several recent works to be suited to tackle the first problem, while algebraic query models have been regarded as appropriate foundations to tackle the second problem. The question however remains how best to put these two models together to have an overall effective system. This thesis aims to exactly fill this gap. We propose a unified query framework to augment automata-style processing with algebra-based query optimization capabilities. We use the automata model to handle the token-oriented streaming XML data and use the algebraic model to support set-oriented optimization techniques. The framework has been designed in two layers such that the logical layer provides a uniform abstraction across the two models and any optimization techniques can be applied in either model uniformly using query rewritings. The physical layer, on the other hand, allows us to refine the implementation details after the logical layer optimization. We have successfully applied this framework in the Raindrop stream processing system. We have identified several trade-offs regarding which query functionality should be realized in which specific query model. We have developed novel optimization techniques to exploit these trade-offs. For example, a query rewrite rule can flexibly push down a pattern matching into the automata model when the optimizer decides that it is more efficient to do so. To deal with incomplete knowledge of source data, we have also developed novel techniques to monitor data statistics, based on which we can apply optimization techniques to choose the optimal query plan at runtime. Our experimental study confirms that considerable performance gains are being achieved when these optimization techniques are applied in our system."

Les entrepôts de données XML forment une base intéressante pour les applications décisionnelles qui exploitent des données hétérogènes et provenant de sources multiples. Cependant, les Systèmes de Gestion de Bases de Données (SGBD) natifs XML actuels présentent des limites en termes de volume de données gérable, d'une part, et de performance des requêtes d'interrogation complexes, d'autre part. Il apparaît donc nécessaire de concevoir des méthodes pour optimiser ces performances.<br /><br />Pour atteindre cet objectif, nous proposons dans ce mémoire de pallier conjointement ces limitations par fragmentation puis par répartition sur une grille de données. Pour cela, nous nous sommes intéressés dans un premier temps à la fragmentation des entrepôts des données XML et nous avons proposé des méthodes qui sont à notre connaissance les premières contributions dans ce domaine. Ces méthodes exploitent une charge de requêtes XQuery pour déduire un schéma de fragmentation horizontale dérivée.<br /><br />Nous avons tout d'abord proposé l'adaptation des techniques les plus efficaces du domaine relationnel aux entrepôts de données XML, puis une méthode de fragmentation originale basée sur la technique de classification k-means. Cette dernière nous a permis de contrôler le nombre de fragments. Nous avons finalement proposé une approche de répartition d'un entrepôt de données XML sur une grille. Ces propositions nous ont amené à proposer un modèle de référence pour les entrepôts de données XML qui unifie et étend les modèles existants dans la littérature.<br /><br />Nous avons finalement choisi de valider nos méthodes de manière expérimentale. Pour cela, nous avons conçu et développé un banc d'essais pour les entrepôts de données XML : XWeB. Les résultats expérimentaux que nous avons obtenus montrent que nous avons atteint notre objectif de maîtriser le volume de données XML et le temps de traitement de requêtes décisionnelles complexes. Ils montrent également que notre méthode de fragmentation basée sur les k-means fournit un gain de performance plus élevé que celui obtenu par les méthodes de fragmentation horizontale dérivée classiques, à la fois en terme de gain de performance et de surcharge des algorithmes.

Die Zope Object Database, kurz ZODB, ist eine Open-Source-Datenbank für Python. Im Gegensatz zu den meisten relationalen Datenbanken verfügt die ZODB allerdings nicht über eine Anfragesprache zur gezielten Selektion von Objekten. <br /> Aufgabe dieser Diplomarbeit ist es, effiziente Ad-Hoc-Anfragemöglichkeiten zu evaluieren und eine geeignete als Zusatzprodukt in Python zu implementieren. <br /> Folgende Themen sind zu bearbeiten: <ul> <li>Vergleich und Auswahl einer Anfragesprache für Objektgraphen</li> <li>Auswahl von Indexstrukturen zur Unterstützung der gewählten Anfragesprache</li> <li>Implementation eines Zusatzprodukts zur ZODB, die eine Anfragesprache sowie unterstützende Indizes bereitstellt</li> <li>Testen und Bewerten der Implementierung</li> </ul>

Cette thèse traite le domaine de coopération des systèmes d'informations basée sur les ontologies. Nous proposons une architecture globale, appelée OWSCIS, qui se base sur les ontologies et les services-web pour la coopération des systèmes d'informations distribués et hétérogènes. Dans cette thèse, nous focalisons sur la problématique de connexion des sources d'informations locales vers des ontologies locales dans le cadre de l'architecture OWSCIS. Cette problématique est articulée en trois axes principaux: 1) la création de l'ontologie locale des sources d'informations locales, 2) la mise en correspondance des sources d'informations locales avec l'ontologie locale, et 3) la traduction des requêtes sur l'ontologie locale vers des requêtes sur les sources d'informations locales. / This thesis treats the area of ontology-based cooperation of information systems. We propose a global architecture called OWSCIS that is based on ontologies and web-services for the cooperation of distributed heterogeneous information systems. In this thesis, we focus on the problem of connecting the local information sources to the local ontologies within OWSCIS architecture. This problem is articulated by three main axes: 1) the creation of the local ontology from the local information sources, 2) the mapping of local information sources to an existing local ontology, and 3) the translation of queries over the local ontologies into queries over local information sources.