Investigation into Indexing XML Data Techniques

The rapid development of XML technology improves the WWW, since the XML data has many advantages and has become a common technology for transferring data cross the internet. Therefore, the objective of this research is to investigate and study the XML indexing techniques in terms of their structures. The main goal of this investigation is to identify the main limitations of these techniques and any other open issues. Furthermore, this research considers most common XML indexing techniques and performs a comparison between them. Subsequently, this work makes an argument to find out these limitations. To conclude, the main problem of all the XML indexing techniques is the trade-off between the size and the efficiency of the indexes. So, all the indexes become large in order to perform well, and none of them is suitable for all users’ requirements. However, each one of these techniques has some advantages in somehow

A survey on tree matching and XML retrieval

International audienceWith the increasing number of available XML documents, numerous approaches for retrieval have been proposed in the literature. They usually use the tree representation of documents and queries to process them, whether in an implicit or explicit way. Although retrieving XML documents can be considered as a tree matching problem between the query tree and the document trees, only a few approaches take advantage of the algorithms and methods proposed by the graph theory. In this paper, we aim at studying the theoretical approaches proposed in the literature for tree matching and at seeing how these approaches have been adapted to XML querying and retrieval, from both an exact and an approximate matching perspective. This study will allow us to highlight theoretical aspects of graph theory that have not been yet explored in XML retrieval

Boosting XML Filtering with a Scalable FPGA-based Architecture

The growing amount of XML encoded data exchanged over the Internet increases the importance of XML based publish-subscribe (pub-sub) and content based routing systems. The input in such systems typically consists of a stream of XML documents and a set of user subscriptions expressed as XML queries. The pub-sub system then filters the published documents and passes them to the subscribers. Pub-sub systems are characterized by very high input ratios, therefore the processing time is critical. In this paper we propose a "pure hardware" based solution, which utilizes XPath query blocks on FPGA to solve the filtering problem. By utilizing the high throughput that an FPGA provides for parallel processing, our approach achieves drastically better throughput than the existing software or mixed (hardware/software) architectures. The XPath queries (subscriptions) are translated to regular expressions which are then mapped to FPGA devices. By introducing stacks within the FPGA we are able to express and process a wide range of path queries very efficiently, on a scalable environment. Moreover, the fact that the parser and the filter processing are performed on the same FPGA chip, eliminates expensive communication costs (that a multi-core system would need) thus enabling very fast and efficient pipelining. Our experimental evaluation reveals more than one order of magnitude improvement compared to traditional pub/sub systems.Comment: CIDR 200

Clustering-based Labelling Scheme - A Hybrid Approach for Efficient Querying and Updating XML Documents

Extensible Markup Language (XML) has become a dominant technology for transferring data through the worldwide web. The XML labelling schemes play a key role in handling XML data efficiently and robustly. Thus, many labelling schemes have been proposed. However, these labelling schemes have limitations and shortcomings. Thus, the aim of this research was to investigate the existing XML labelling schemes and their limitations in order to address the issue of efficiency of XML query performance. This thesis investigated the existing labelling schemes and classified them into three categories based on certain criteria, in order to identify the limitations and challenges of these labelling schemes. Based on the outcomes of this investigation, this thesis proposed a state-of-theart labelling scheme, called clustering-based labelling scheme, to resolve or improve the key limitations such as the efficiency of the XML query processing, labelling XML nodes, and XML updates cost. This thesis argued that using certain existing labelling schemes to label nodes, and using the clustering-based techniques can improve query and labelling nodes efficiency. Theoretically, the proposed scheme is based on dividing the nodes of an XML document into clusters. Two existing labelling schemes, which are the Dewey and LLS labelling schemes, were selected for labelling these clusters and their nodes. Subsequently, the proposed scheme was designed and implemented. In addition, the Dewey and LLS labelling scheme were implemented for the purpose of evaluating the proposed scheme. Subsequently, four experiments were designed in order to test the proposed scheme against the Dewey and LLS labelling schemes. The results of these experiments suggest that the proposed scheme achieved better results than the Dewey and LLS schemes. Consequently, the research hypothesis was accepted overall with few exceptions, and the proposed scheme showed an improvement in the performance and all the targeted features and aspects

Fachlich erweiterbare 3D-Stadtmodelle – Management, Visualisierung und Interaktion

Domain-extendable semantic 3D city models are complex mappings and inventories of the urban environment which can be utilized as an integrative information backbone to facilitate a range of application fields like urban planning, environmental simulations, disaster management, and energy assessment. Today, more and more countries and cities worldwide are creating their own 3D city models based on the CityGML specification which is an international standard issued by the Open Geospatial Consortium (OGC) to provide an open data model and XML-based format for describing the relevant urban objects with regards to their 3D geometry, topology, semantics, and appearance. It especially provides a flexible and systematic extension mechanism called “Application Domain Extension (ADE)” which allows third parties to dynamically extend the existing CityGML definitions with additional information models from different application domains for representing the extended or newly introduced geographic object types within a common framework. However, due to the consequent large size and high model complexity, the practical utilization of country-wide CityGML datasets has posed a tremendous challenge regarding the setup of an extensive application system to support the efficient data storage, analysis, management, interaction, and visualization. These requirements have been partly solved by the existing free 3D geo-database solution called ‘3D City Database (3DCityDB)’ which offers a rich set of functionalities for dealing with standard CityGML data models, but lacked the support for CityGML ADEs. The key motivation of this thesis is to develop a reliable approach for extending the existing database solution to support the efficient management, visualization, and interaction of large geospatial data elements of arbitrary CityGML ADEs. Emphasis is first placed on answering the question of how to dynamically extend the relational database schema by parsing and interpreting the XML schema files of the ADE and dynamically create new database tables accordingly. Based on a comprehensive survey of the related work, a new graph-based framework has been proposed which uses typed and attributed graphs for semantically representing the object-oriented data models of CityGML ADEs and utilizes graph transformation systems to automatically generate compact table structures extending the 3DCityDB. The transformation process is performed by applying a series of fine-grained graph transformation rules which allow users to declaratively describe the complex mapping rules including the optimization concepts that are employed in the development of the 3DCityDB database schema. The second major contribution of this thesis is the development of a new multi-level system which can serve as a complete and integrative platform for facilitating the various analysis, simulation, and modification operations on the complex-structured 3D city models based on CityGML and 3DCityDB. It introduces an additional application level based on a so-called ‘app-concept’ that allows for constructing a light-weight web application to reach a good balance between the high data model complexity and the specific application requirements of the end users. Each application can be easily built on top of a developed 3D web client whose functionalities go beyond the efficient 3D geo-visualization and interactive exploration, and also allows for performing collaborative modifications and analysis of 3D city models by taking advantage of the Cloud Computing technology. This multi-level system along with the extended 3DCityDB have been successfully utilized and evaluated by many practical projects.Fachlich erweiterbare semantische 3D-Stadtmodelle sind komplexe Abbildungen und Datenbestände der städtischen Umgebung, die als ein integratives Informationsrückgrat genutzt werden können, um eine Reihe von Anwendungsfeldern wie z. B. Stadtplanung, Umweltsimulationen, Katastrophenmanagement und Energiebewertung zu ermöglichen. Heute schaffen immer mehr Länder und Städte weltweit ihre eigenen 3D-Stadtmodelle auf Basis des internationalen Standards CityGML des Open Geospatial Consortium (OGC), um ein offenes Datenmodell und ein XML-basiertes Format zur Beschreibung der relevanten Stadtobjekte in Bezug auf ihre 3D-Geometrien, Topologien, Semantik und Erscheinungen zur Verfügung zu stellen. Es bietet insbesondere einen flexiblen und systematischen Erweiterungsmechanismus namens „Application Domain Extension“ (ADE), der es Dritten ermöglicht, die bestehenden CityGML-Definitionen mit zusätzlichen Informationsmodellen aus verschiedenen Anwendungsdomänen dynamisch zu erweitern, um die erweiterten oder neu eingeführten Stadtobjekt-Typen innerhalb eines gemeinsamen Framework zu repräsentieren. Aufgrund der konsequent großen Datenmenge und hohen Modellkomplexität bei der praktischen Nutzung der landesweiten CityGML-Datensätze wurden jedoch enorme Anforderungen an den Aufbau eines umfangreichen Anwendungssystems zur Unterstützung der effizienten Speicherung, Analyse, Verwaltung, Interaktion und Visualisierung der Daten gestellt. Die bestehende kostenlose 3D-Geodatenbank-Lösung „3D City Database“ (3DCityDB) entsprach bereits teilweise diesen Anforderungen, indem sie zwar eine umfangreiche Funktionalität für den Umgang mit den Standard-CityGML-Datenmodellen, jedoch keine Unterstützung für CityGML-ADEs bietet. Die Schlüsselmotivation für diese Arbeit ist es, einen zuverlässigen Ansatz zur Erweiterung der bestehenden Datenbanklösung zu entwickeln, um das effiziente Management, die Visualisierung und Interaktion großer Datensätze beliebiger CityGML-ADEs zu unterstützen. Der Schwerpunkt liegt zunächst auf der Beantwortung der Schlüsselfrage, wie man das relationale Datenbankschema dynamisch erweitern kann, indem die XML-Schemadateien der ADE analysiert und interpretiert und anschließend dem entsprechende neue Datenbanktabellen erzeugt werden. Auf Grundlage einer umfassenden Studie verwandter Arbeiten wurde ein neues graphbasiertes Framework entwickelt, das die typisierten und attributierten Graphen zur semantischen Darstellung der objektorientierten Datenmodelle von CityGML-ADEs verwendet und anschließend Graphersetzungssysteme nutzt, um eine kompakte Tabellenstruktur zur Erweiterung der 3DCityDB zu generieren. Der Transformationsprozess wird durch die Anwendung einer Reihe feingranularer Graphersetzungsregeln durchgeführt, die es Benutzern ermöglicht, die komplexen Mapping-Regeln einschließlich der Optimierungskonzepte aus der Entwicklung des 3DCityDB-Datenbankschemas deklarativ zu formalisieren. Der zweite wesentliche Beitrag dieser Arbeit ist die Entwicklung eines neuen mehrstufigen Systemkonzepts, das auf CityGML und 3DCityDB basiert und gleichzeitig als eine komplette und integrative Plattform zur Erleichterung der Analyse, Simulationen und Modifikationen der komplex strukturierten 3D-Stadtmodelle dienen kann. Das Systemkonzept enthält eine zusätzliche Anwendungsebene, die auf einem sogenannten „App-Konzept“ basiert, das es ermöglicht, eine leichtgewichtige Applikation bereitzustellen, die eine gute Balance zwischen der hohen Modellkomplexität und den spezifischen Anwendungsanforderungen der Endbenutzer erreicht. Jede Applikation lässt sich ganz einfach mittels eines bereits entwickelten 3D-Webclients aufbauen, dessen Funktionalitäten über die effiziente 3D-Geo-Visualisierung und interaktive Exploration hinausgehen und auch die Durchführung kollaborativer Modifikationen und Analysen von 3D-Stadtmodellen mit Hilfe von der Cloud-Computing-Technologie ermöglichen. Dieses mehrstufige System zusammen mit dem erweiterten 3DCityDB wurde erfolgreich in vielen praktischen Projekten genutzt und bewertet

Fachlich erweiterbare 3D-Stadtmodelle – Management, Visualisierung und Interaktion

Domain-extendable semantic 3D city models are complex mappings and inventories of the urban environment which can be utilized as an integrative information backbone to facilitate a range of application fields like urban planning, environmental simulations, disaster management, and energy assessment. Today, more and more countries and cities worldwide are creating their own 3D city models based on the CityGML specification which is an international standard issued by the Open Geospatial Consortium (OGC) to provide an open data model and XML-based format for describing the relevant urban objects with regards to their 3D geometry, topology, semantics, and appearance. It especially provides a flexible and systematic extension mechanism called “Application Domain Extension (ADE)” which allows third parties to dynamically extend the existing CityGML definitions with additional information models from different application domains for representing the extended or newly introduced geographic object types within a common framework. However, due to the consequent large size and high model complexity, the practical utilization of country-wide CityGML datasets has posed a tremendous challenge regarding the setup of an extensive application system to support the efficient data storage, analysis, management, interaction, and visualization. These requirements have been partly solved by the existing free 3D geo-database solution called ‘3D City Database (3DCityDB)’ which offers a rich set of functionalities for dealing with standard CityGML data models, but lacked the support for CityGML ADEs. The key motivation of this thesis is to develop a reliable approach for extending the existing database solution to support the efficient management, visualization, and interaction of large geospatial data elements of arbitrary CityGML ADEs. Emphasis is first placed on answering the question of how to dynamically extend the relational database schema by parsing and interpreting the XML schema files of the ADE and dynamically create new database tables accordingly. Based on a comprehensive survey of the related work, a new graph-based framework has been proposed which uses typed and attributed graphs for semantically representing the object-oriented data models of CityGML ADEs and utilizes graph transformation systems to automatically generate compact table structures extending the 3DCityDB. The transformation process is performed by applying a series of fine-grained graph transformation rules which allow users to declaratively describe the complex mapping rules including the optimization concepts that are employed in the development of the 3DCityDB database schema. The second major contribution of this thesis is the development of a new multi-level system which can serve as a complete and integrative platform for facilitating the various analysis, simulation, and modification operations on the complex-structured 3D city models based on CityGML and 3DCityDB. It introduces an additional application level based on a so-called ‘app-concept’ that allows for constructing a light-weight web application to reach a good balance between the high data model complexity and the specific application requirements of the end users. Each application can be easily built on top of a developed 3D web client whose functionalities go beyond the efficient 3D geo-visualization and interactive exploration, and also allows for performing collaborative modifications and analysis of 3D city models by taking advantage of the Cloud Computing technology. This multi-level system along with the extended 3DCityDB have been successfully utilized and evaluated by many practical projects.Fachlich erweiterbare semantische 3D-Stadtmodelle sind komplexe Abbildungen und Datenbestände der städtischen Umgebung, die als ein integratives Informationsrückgrat genutzt werden können, um eine Reihe von Anwendungsfeldern wie z. B. Stadtplanung, Umweltsimulationen, Katastrophenmanagement und Energiebewertung zu ermöglichen. Heute schaffen immer mehr Länder und Städte weltweit ihre eigenen 3D-Stadtmodelle auf Basis des internationalen Standards CityGML des Open Geospatial Consortium (OGC), um ein offenes Datenmodell und ein XML-basiertes Format zur Beschreibung der relevanten Stadtobjekte in Bezug auf ihre 3D-Geometrien, Topologien, Semantik und Erscheinungen zur Verfügung zu stellen. Es bietet insbesondere einen flexiblen und systematischen Erweiterungsmechanismus namens „Application Domain Extension“ (ADE), der es Dritten ermöglicht, die bestehenden CityGML-Definitionen mit zusätzlichen Informationsmodellen aus verschiedenen Anwendungsdomänen dynamisch zu erweitern, um die erweiterten oder neu eingeführten Stadtobjekt-Typen innerhalb eines gemeinsamen Framework zu repräsentieren. Aufgrund der konsequent großen Datenmenge und hohen Modellkomplexität bei der praktischen Nutzung der landesweiten CityGML-Datensätze wurden jedoch enorme Anforderungen an den Aufbau eines umfangreichen Anwendungssystems zur Unterstützung der effizienten Speicherung, Analyse, Verwaltung, Interaktion und Visualisierung der Daten gestellt. Die bestehende kostenlose 3D-Geodatenbank-Lösung „3D City Database“ (3DCityDB) entsprach bereits teilweise diesen Anforderungen, indem sie zwar eine umfangreiche Funktionalität für den Umgang mit den Standard-CityGML-Datenmodellen, jedoch keine Unterstützung für CityGML-ADEs bietet. Die Schlüsselmotivation für diese Arbeit ist es, einen zuverlässigen Ansatz zur Erweiterung der bestehenden Datenbanklösung zu entwickeln, um das effiziente Management, die Visualisierung und Interaktion großer Datensätze beliebiger CityGML-ADEs zu unterstützen. Der Schwerpunkt liegt zunächst auf der Beantwortung der Schlüsselfrage, wie man das relationale Datenbankschema dynamisch erweitern kann, indem die XML-Schemadateien der ADE analysiert und interpretiert und anschließend dem entsprechende neue Datenbanktabellen erzeugt werden. Auf Grundlage einer umfassenden Studie verwandter Arbeiten wurde ein neues graphbasiertes Framework entwickelt, das die typisierten und attributierten Graphen zur semantischen Darstellung der objektorientierten Datenmodelle von CityGML-ADEs verwendet und anschließend Graphersetzungssysteme nutzt, um eine kompakte Tabellenstruktur zur Erweiterung der 3DCityDB zu generieren. Der Transformationsprozess wird durch die Anwendung einer Reihe feingranularer Graphersetzungsregeln durchgeführt, die es Benutzern ermöglicht, die komplexen Mapping-Regeln einschließlich der Optimierungskonzepte aus der Entwicklung des 3DCityDB-Datenbankschemas deklarativ zu formalisieren. Der zweite wesentliche Beitrag dieser Arbeit ist die Entwicklung eines neuen mehrstufigen Systemkonzepts, das auf CityGML und 3DCityDB basiert und gleichzeitig als eine komplette und integrative Plattform zur Erleichterung der Analyse, Simulationen und Modifikationen der komplex strukturierten 3D-Stadtmodelle dienen kann. Das Systemkonzept enthält eine zusätzliche Anwendungsebene, die auf einem sogenannten „App-Konzept“ basiert, das es ermöglicht, eine leichtgewichtige Applikation bereitzustellen, die eine gute Balance zwischen der hohen Modellkomplexität und den spezifischen Anwendungsanforderungen der Endbenutzer erreicht. Jede Applikation lässt sich ganz einfach mittels eines bereits entwickelten 3D-Webclients aufbauen, dessen Funktionalitäten über die effiziente 3D-Geo-Visualisierung und interaktive Exploration hinausgehen und auch die Durchführung kollaborativer Modifikationen und Analysen von 3D-Stadtmodellen mit Hilfe von der Cloud-Computing-Technologie ermöglichen. Dieses mehrstufige System zusammen mit dem erweiterten 3DCityDB wurde erfolgreich in vielen praktischen Projekten genutzt und bewertet

Semantics and efficient evaluation of partial tree-pattern queries on XML

Current applications export and exchange XML data on the web. Usually, XML data are queried using keyword queries or using the standard structured query language XQuery the core of which consists of the navigational query language XPath. In this context, one major challenge is the querying of the data when the structure of the data sources is complex or not fully known to the user. Another challenge is the integration of multiple data sources that export data with structural differences and irregularities. In this dissertation, a query language for XML called Partial Tree-Pattern Query (PTPQ) language is considered. PTPQs generalize and strictly contain Tree-Pattern Queries (TPQs) and can express a broad structural fragment of XPath. Because of their expressive power and flexibility, they are useful for querying XML documents the structure of which is complex or not fully known to the user, and for integrating XML data sources with different structures. The dissertation focuses on three issues. The first one is the design of efficient non-main-memory evaluation methods for PTPQs. The second one is the assignment of semantics to PTPQs so that they return meaningful answers. The third one is the development of techniques for answering TPQs using materialized views. Non-main-memory XML query evaluation can be done in two modes (which also define two evaluation models). In the first mode, data is preprocessed and indexes, called inverted lists, are built for it. In the second mode, data are unindexed and arrives continuously in the form of a stream. Existing algorithms cannot be used directly or indirectly to efficiently compute PTPQs in either mode. Initially, the problem of efficiently evaluating partial path queries in the inverted lists model has been addressed. Partial path queries form a subclass of PTPQs which is not contained in the class of TPQs. Three novel algorithms for evaluating partial path queries including a holistic one have been designed. The analytical and experimental results show that the holistic algorithm outperforms the other two. These results have been extended into holistic and non-holistic approaches for PTPQs in the inverted lists model. The experiments show again the superiority of the holistic approach. The dissertation has also addressed the problem of evaluating PTPQs in the streaming model, and two original efficient streaming algorithms for PTPQs have been designed. Compared to the only known streaming algorithm that supports an extension of TPQs, the experimental results show that the proposed algorithms perform better by orders of magnitude while consuming a much smaller fraction of memory space. An original approach for assigning semantics to PTPQs has also been devised. The novel semantics seamlessly applies to keyword queries and to queries with structural restrictions. In contrast to previous approaches that operate locally on data, the proposed approach operates globally on structural summaries of data to extract tree patterns. Compared to previous approaches, an experimental evaluation shows that our approach has a perfect recall both for XML documents with complete and with incomplete data. It also shows better precision compared to approaches with similar recall. Finally, the dissertation has addressed the problem of answering XML queries using exclusively materialized views. An original approach for materializing views in the context of the inverted lists model has been suggested. Necessary and sufficient conditions have been provided for tree-pattern query answerability in terms of view-to-query homomorphisms. A time and space efficient algorithm was designed for deciding query answerability and a technique for computing queries over view materializations using stack- based holistic algorithms was developed. Further, optimizations were developed which (a) minimize the storage space and avoid redundancy by materializing views as bitmaps, and (b) optimize the evaluation of the queries over the views by applying bitwise operations on view materializations. The experimental results show that the proposed approach obtains largely higher hit rates than previous approaches, speeds up significantly the evaluation of queries without using views, and scales very smoothly in terms of storage space and computational overhead

Novel computational techniques for mapping and classifying Next-Generation Sequencing data

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up

Querying and Updating XML Data based on Node Labeling Schemes

Ph.DDOCTOR OF PHILOSOPH

Approximate Assertional Reasoning Over Expressive Ontologies

In this thesis, approximate reasoning methods for scalable assertional reasoning are provided whose computational properties can be established in a well-understood way, namely in terms of soundness and completeness, and whose quality can be analyzed in terms of statistical measurements, namely recall and precision. The basic idea of these approximate reasoning methods is to speed up reasoning by trading off the quality of reasoning results against increased speed