A Survey on Mapping Semi-Structured Data and Graph Data to Relational Data

The data produced by various services should be stored and managed in an appropriate format for gaining valuable knowledge conveniently. This leads to the emergence of various data models, including relational, semi-structured, and graph models, and so on. Considering the fact that the mature relational databases established on relational data models are still predominant in today's market, it has fueled interest in storing and processing semi-structured data and graph data in relational databases so that mature and powerful relational databases' capabilities can all be applied to these various data. In this survey, we review existing methods on mapping semi-structured data and graph data into relational tables, analyze their major features, and give a detailed classification of those methods. We also summarize the merits and demerits of each method, introduce open research challenges, and present future research directions. With this comprehensive investigation of existing methods and open problems, we hope this survey can motivate new mapping approaches through drawing lessons from eachmodel's mapping strategies, aswell as a newresearch topic - mapping multi-model data into relational tables.Peer reviewe

A Nine Month Progress Report on an Investigation into Mechanisms for Improving Triple Store Performance

This report considers the requirement for fast, efficient, and scalable triple stores as part of the effort to produce the Semantic Web. It summarises relevant information in the major background field of Database Management Systems (DBMS), and provides an overview of the techniques currently in use amongst the triple store community. The report concludes that for individuals and organisations to be willing to provide large amounts of information as openly-accessible nodes on the Semantic Web, storage and querying of the data must be cheaper and faster than it is currently. Experiences from the DBMS field can be used to maximise triple store performance, and suggestions are provided for lines of investigation in areas of storage, indexing, and query optimisation. Finally, work packages are provided describing expected timetables for further study of these topics

Physical database design in document stores

Tesi en modalitat de cotutela, Universitat Politècnica de Catalunya i Université libre de BruxellesNoSQL is an umbrella term used to classify alternate storage systems to the traditional Relational Database Management Systems (RDBMSs). Among these, Document stores have gained popularity mainly due to the semi-structured data storage model and the rich query capabilities. They encourage users to use a data-first approach as opposed to a design-first one. Database design on document stores is mainly carried out in a trial-and-error or ad-hoc rule-based manner instead of a formal process such as normalization in an RDBMS. However, these approaches could easily lead to a non-optimal design resulting additional costs in the long run. This PhD thesis aims to provide a novel multi-criteria-based approach to database design in document stores. Most of such existing approaches are based on optimizing query performance. However, other factors include storage requirement and complexity of the stored documents specific to each use case. There is a large solution space of alternative designs due to the different combinations of referencing and nesting of data. Thus, we believe multi-criteria optimization is ideal to solve this problem. To achieve this, we need to address several issues that will enable us to apply multi-criteria optimization for the data design problem. First, we evaluate the impact of alternate storage representations of semi-structured data. There are multiple and equivalent ways to physically represent semi-structured data, but there is a lack of evidence about the potential impact on space and query performance. Thus, we embark on the task of quantifying that precisely for document stores. We empirically compare multiple ways of representing semi-structured data, allowing us to derive a set of guidelines for efficient physical database design considering both JSON and relational options in the same palette. Then, we need a formal canonical model that can represent alternative designs. We propose a hypergraph-based approach for representing heterogeneous datastore designs. We extend and formalize an existing common programming interface to NoSQL systems as hypergraphs. We define design constraints and query transformation rules for representative data store types. Next, we propose a simple query rewriting algorithm and provide a prototype implementation together with storage statistics estimator. Next, we require a formal query cost model to estimate and evaluate query performance on alternative document store designs. Document stores use primitive approaches to query processing, such as relying on the end-user to specify the usage of indexes instead of a formal cost model. But we require a reliable approach to compare alternative designs on how they perform on a specific query. For this, we define a generic storage and query cost model based on disk access and memory allocation. As all document stores carry out data operations in memory, we first estimate the memory usage by considering the characteristics of the stored documents, their access patterns, and memory management algorithms. Then, using this estimation and metadata storage size, we introduce a cost model for random access queries. We validate our work on two well-known document store implementations. The results show that the memory usage estimates have an average precision of 91% and predicted costs are highly correlated to the actual execution times. During this work, we also managed to suggest several improvements to document stores. Finally, we implement the automated database design solution using multi-criteria optimization. We introduce an algebra of transformations that can systematically modify a design of our canonical representation. Then, using them, we implement a local search algorithm driven by a loss function that can propose near-optimal designs with high probability. We compare our prototype against an existing document store data design solution. Our proposed designs have better performance and are more compact with less redundancy.NoSQL descriu sistemes d'emmagatzematge alternatius als tradicionals de gestió de bases de dades relacionals (RDBMS). Entre aquests, els magatzems de documents han guanyat popularitat principalment a causa del model de dades semiestructurat i les riques capacitats de consulta. Animen els usuaris a utilitzar un enfocament de dades primer, en lloc d'un enfocament de disseny primer. El disseny de dades en magatzems de documents es porta a terme principalment en forma d'assaig-error o basat en regles ad-hoc en lloc d'un procés formal i sistemàtic com ara la normalització en un RDBMS. Aquest enfocament condueix fàcilment a un disseny no òptim que generarà costos addicionals a llarg termini. La majoria dels enfocaments existents es basen en l'optimització del rendiment de les consultes. Aquesta tesi pretén, en canvi, proporcionar un nou enfocament basat en diversos criteris per al disseny de bases de dades en magatzems de documents, inclouen el requisit d'espai i la complexitat dels documents emmagatzemats específics per a cada cas d'ús. En general, hi ha un gran espai de solucions de dissenys alternatives. Per tant, creiem que l'optimització multicriteri és ideal per resoldre aquest problema. Per aconseguir-ho, hem d'abordar diversos problemes que ens permetran aplicar l'optimització multicriteri. En primer, avaluem l'impacte de les representacions alternatives de dades semiestructurades. Hi ha maneres múltiples i equivalents de representar dades semiestructurades, però hi ha una manca d'evidència sobre l'impacte potencial en l'espai i el rendiment de les consultes. Així, ens embarquem en la tasca de quantificar-ho. Comparem empíricament múltiples representacions de dades semiestructurades, cosa que ens permet derivar directrius per a un disseny eficient tenint en compte les opcions dels JSON i relacionals alhora. Aleshores, necessitem un model canònic que pugui representar dissenys alternatius i proposem un enfocament basat en hipergrafs. Estenem i formalitzem una interfície de programació comuna existent als sistemes NoSQL com a hipergrafs. Definim restriccions de disseny i regles de transformació de consultes per a tipus de magatzem de dades representatius. A continuació, proposem un algorisme de reescriptura de consultes senzill i proporcionem una implementació juntament amb un estimador d'estadístiques d'emmagatzematge. Els magatzems de documents utilitzen enfocaments primitius per al processament de consultes, com ara confiar en l'usuari final per especificar l'ús d'índexs en lloc d'un model de cost. Conseqüentment, necessitem un model de cost de consulta per estimar i avaluar el rendiment en dissenys alternatius. Per això, definim un model genèric propi basat en l'accés a disc i l'assignació de memòria. Com que tots els magatzems de documents duen a terme operacions de dades a memòria, primer estimem l'ús de la memòria tenint en compte les característiques dels documents emmagatzemats, els seus patrons d'accés i els algorismes de gestió de memòria. A continuació, utilitzant aquesta estimació i la mida d'emmagatzematge de metadades, introduïm un model de costos per a consultes d'accés aleatori. Validem el nostre treball en dues implementacions conegudes. Els resultats mostren que les estimacions d'ús de memòria tenen una precisió mitjana del 91% i els costos previstos estan altament correlacionats amb els temps d'execució reals. Finalment, implementem la solució de disseny automatitzat de bases de dades mitjançant l'optimització multicriteri. Introduïm una àlgebra de transformacions que pot modificar sistemàticament un disseny en la nostra representació canònica. A continuació, utilitzant-la, implementem un algorisme de cerca local impulsat per una funció de pèrdua que pot proposar dissenys gairebé òptims amb alta probabilitat. Comparem el nostre prototip amb una solució de disseny de dades de magatzem de documents existent. Els nostres dissenys proposats tenen un millor rendiment i són més compactes, amb menys redundànciaNoSQL est un terme générique utilisé pour classer les systèmes de stockage alternatifs aux systèmes de gestion de bases de données relationnelles (SGBDR) traditionnels. Au moment de la rédaction de cet article, il existe plus de 200 systèmes NoSQL disponibles qui peuvent être classés en quatre catégories principales sur le modèle de stockage de données : magasins de valeurs-clés, magasins de documents, magasins de familles de colonnes et magasins de graphiques. Les magasins de documents ont gagné en popularité principalement en raison du modèle de stockage de données semi-structuré et des capacités de requêtes riches par rapport aux autres systèmes NoSQL, ce qui en fait un candidat idéal pour le prototypage rapide. Les magasins de documents encouragent les utilisateurs à utiliser une approche axée sur les données plutôt que sur la conception. La conception de bases de données sur les magasins de documents est principalement effectuée par essais et erreurs ou selon des règles ad hoc plutôt que par un processus formel tel que la normalisation dans un SGBDR. Cependant, ces approches pourraient facilement conduire à une conception de base de données non optimale entraînant des coûts supplémentaires de traitement des requêtes, de stockage des données et de refonte. Cette thèse de doctorat vise à fournir une nouvelle approche multicritère de la conception de bases de données dans les magasins de documents. La plupart des approches existantes de conception de bases de données sont basées sur l’optimisation des performances des requêtes. Cependant, d’autres facteurs incluent les exigences de stockage et la complexité des documents stockés spécifique à chaque cas d’utilisation. De plus, il existe un grand espace de solution de conceptions alternatives en raison des différentes combinaisons de référencement et d’imbrication des données. Par conséquent, nous pensons que l’optimisation multicritères est idéale par l’intermédiaire d’une expérience éprouvée dans la résolution de tels problèmes dans divers domaines. Cependant, pour y parvenir, nous devons résoudre plusieurs problèmes qui nous permettront d’appliquer une optimisation multicritère pour le problème de conception de données. Premièrement, nous évaluons l’impact des représentations alternatives de stockage des données semi-structurées. Il existe plusieurs manières équivalentes de représenter physiquement des données semi-structurées, mais il y a un manque de preuves concernant l’impact potentiel sur l’espace et sur les performances des requêtes. Ainsi, nous nous lançons dans la tâche de quantifier cela précisément pour les magasins de documents. Nous comparons empiriquement plusieurs façons de représenter des données semi-structurées, ce qui nous permet de dériver un ensemble de directives pour une conception de base de données physique efficace en tenant compte à la fois des options JSON et relationnelles dans la même palette. Ensuite, nous avons besoin d’un modèle canonique formel capable de représenter des conceptions alternatives. Dans cette mesure, nous proposons une approche basée sur des hypergraphes pour représenter des conceptions de magasins de données hétérogènes. Prenant une interface de programmation commune existante aux systèmes NoSQL, nous l’étendons et la formalisons sous forme d’hypergraphes. Ensuite, nous définissons les contraintes de conception et les règles de transformation des requêtes pour trois types de magasins de données représentatifs. Ensuite, nous proposons un algorithme de réécriture de requête simple à partir d’un algorithme générique dans un magasin de données sous-jacent spécifique et fournissons une implémentation prototype. De plus, nous introduisons un estimateur de statistiques de stockage sur les magasins de données sous-jacents. Enfin, nous montrons la faisabilité de notre approche sur un cas d’utilisation d’un système polyglotte existant ainsi que son utilité dans les calculs de métadonnées et de chemins de requêtes physiques. Ensuite, nous avons besoin d’un modèle de coûts de requêtes formel pour estimer et évaluer les performances des requêtes sur des conceptions alternatives de magasin de documents. Les magasins de documents utilisent des approches primitives du traitement des requêtes, telles que l’évaluation de tous les plans de requête possibles pour trouver le plan gagnant et son utilisation dans les requêtes similaires ultérieures, ou l’appui sur l’usager final pour spécifier l’utilisation des index au lieu d’un modèle de coûts formel. Cependant, nous avons besoin d’une approche fiable pour comparer deux conceptions alternatives sur la façon dont elles fonctionnent sur une requête spécifique. Pour cela, nous définissons un modèle de coûts de stockage et de requête générique basé sur l’accès au disque et l’allocation de mémoire qui permet d’estimer l’impact des décisions de conception. Étant donné que tous les magasins de documents effectuent des opérations sur les données en mémoire, nous estimons d’abord l’utilisation de la mémoire en considérant les caractéristiques des documents stockés, leurs modèles d’accès et les algorithmes de gestion de la mémoire. Ensuite, en utilisant cette estimation et la taille de stockage des métadonnées, nous introduisons un modèle de coûts pour les requêtes à accès aléatoire. Il s’agit de la première tenta ive d’une telle approche au meilleur de notre connaissance. Enfin, nous validons notre travail sur deux implémentations de magasin de documents bien connues : MongoDB et Couchbase. Les résultats démontrent que les estimations d’utilisation de la mémoire ont une précision moyenne de 91% et que les coûts prévus sont fortement corrélés aux temps d’exécution réels. Au cours de ce travail, nous avons réussi à proposer plusieurs améliorations aux systèmes de stockage de documents. Ainsi, ce modèle de coûts contribue également à identifier les discordances entre les implémentations de stockage de documents et leurs attentes théoriques. Enfin, nous implémentons la solution de conception automatisée de bases de données en utilisant l’optimisation multicritères. Tout d’abord, nous introduisons une algèbre de transformations qui peut systématiquement modifier une conception de notre représentation canonique. Ensuite, en utilisant ces transformations, nous implémentons un algorithme de recherche locale piloté par une fonction de perte qui peut proposer des conceptions quasi optimales avec une probabilité élevée. Enfin, nous comparons notre prototype à une solution de conception de données de magasin de documents existante uniquement basée sur le coût des requêtes. Nos conceptions proposées ont de meilleures performances et sont plus compactes avec moins de redondancePostprint (published version

Storage, Querying and Inferencing for Semantic Web Languages

Harmelen, F.A.H. van [Promotor

AT-GIS: highly parallel spatial query processing with associative transducers

Users in many domains, including urban planning, transportation, and environmental science want to execute analytical queries over continuously updated spatial datasets. Current solutions for largescale spatial query processing either rely on extensions to RDBMS, which entails expensive loading and indexing phases when the data changes, or distributed map/reduce frameworks, running on resource-hungry compute clusters. Both solutions struggle with the sequential bottleneck of parsing complex, hierarchical spatial data formats, which frequently dominates query execution time. Our goal is to fully exploit the parallelism offered by modern multicore CPUs for parsing and query execution, thus providing the performance of a cluster with the resources of a single machine. We describe AT-GIS, a highly-parallel spatial query processing system that scales linearly to a large number of CPU cores. ATGIS integrates the parsing and querying of spatial data using a new computational abstraction called associative transducers(ATs). ATs can form a single data-parallel pipeline for computation without requiring the spatial input data to be split into logically independent blocks. Using ATs, AT-GIS can execute, in parallel, spatial query operators on the raw input data in multiple formats, without any pre-processing. On a single 64-core machine, AT-GIS provides 3× the performance of an 8-node Hadoop cluster with 192 cores for containment queries, and 10× for aggregation queries

An XML-based framework for electronic business document integration with relational databases

Small and medium enterprises (SMEs) are becoming increasingly engaged in B2B interactions. The ubiquitousness of the Internet and the quasi-reliance on electronic document exchanges with larger trading partners have fostered this move. The main technical challenge that this brings to SMEs is that of business document integration: they need to exchange business documents with heterogeneous document formats and also integrate these documents with internal information systems. Often they can not afford using expensive, customized and proprietary solutions for document exchange and storage. Rather they need cost-effective approaches designed based on open standards and backed with easy-to-use information systems. In this dissertation, we investigate the problem of business document integration for SMEs following a design science methodology. We propose a framework and conceptual architecture for a business document integration system (BDIS). By studying existing business document formats, we recommend using the GS1 XML standard format as the intermediate format for business documents in BDIS. The GS1 standards are widely used in supply chains and logistics globally. We present an architecture for BDIS consisting of two layers: one for the design of internal information system based on relational databases, capable of storing XML business documents, and the other enabling the exchange of heterogeneous business documents at runtime. For the design layer, we leverage existing XML schema conversion approaches, and extend them, to propose a customized and novel approach for converting GS1 XML document schemas into relational schemas. For the runtime layer, we propose wrappers as architectural components for the conversion of various electronic documents formats into the GS1 XML format. We demonstrate our approach through a case study involving a GS1 XML business document. We have implemented a prototype BDIS. We have evaluated and compared it with existing research and commercial tools for XML to relational schema conversion. The results show that it generates operational and simpler relational schemas for GS1 XML documents. In conclusion, the proposed framework enables SMEs to engage effectively in electronic business

Dynamic web forms development using RuleML. Building a framework using metadata driven rules to control Web forms generation and appearance.

Web forms development for Web based applications is often expensive, laborious, error-prone, time consuming and requires a lot of effort. Web forms are used by many different people with different backgrounds and a lot of demands. There is a very high cost associated with the need to update the Web application systems to achieve these demands. A wide range of techniques and ideas to automate the generation of Web forms exist. These techniques and ideas however, are not capable of generating the most dynamic behaviour of form elements, and make Insufficient use of database metadata to control Web forms¿ generation and appearance. In this thesis different techniques are proposed that use RuleML and database metadata to build rulebases to improve the automatic and dynamic generation of Web forms. First this thesis proposes the use of a RuleML format rulebase using Reaction RuleML that can be used to support the development of automated Web interfaces. Database metadata can be extracted from system catalogue tables in typical relational database systems, and used in conjunction with the rulebase to produce appropriate Web form elements. Results show that this mechanism successfully insulates application logic from code and suggests that Abstract iii the method can be extended from generic metadata rules to more domain specific rules. Second it proposes the use of common sense rules and domain specific rules rulebases using Reaction RuleML format in conjunction with database metadata rules to extend support for the development of automated Web forms. Third it proposes the use of rules that involve code to implement more semantics for Web forms. Separation between content, logic and presentation of Web applications has become an important issue for faster development and easy maintenance. Just as CSS applied on the client side to control the overall presentation of Web applications, a set of rules can give a similar consistency to the appearance and operation of any set of forms that interact with the same database. We develop rules to order Web form elements and query forms using Reaction RuleML format in conjunction with database metadata rules. The results show the potential of RuleML formats for representing database structural and active semantics. Fourth it proposes the use of a RuleML based approach to provide more support for greater semantics for example advanced domain support even when this is not a DBMS feature. The approach is to specify most of the semantics associated with data stored in RDBMS, to overcome some RDBMSs limitations. RuleML could be used to represent database metadata as an external format

CELO: A System for Efficiently Building Informatics Solutions to Manage Biomedical Research Data

Traditional data management methods are unable to sufficiently support growing trends in biomedical research such as collection of larger data sets, use of diverse data types, and sharing of data among multiple laboratories. Although many technologies are readily available to help laboratories build data management solutions, many laboratories are not taking advantage of them. This may be due to hardware and software costs, the need for an informaticist to build customized solutions, and long development times. Several systems already exist which attempt to address the informatics needs of biomedical researchers. A review of these systems has revealed the benefits and drawbacks of various system design approaches, and has helped us to identify a set of core requirements for a system that will successfully serve the biomedical research community. In consideration of these requirements, we developed the Customizable Electronic Laboratory Online (CELO) system to help laboratories efficiently build cost-effective informatics solutions. CELO automatically creates a generic database and web interface for laboratories that submit a simple web registration form. Researchers can then build their own customized data management systems using web-based features such as configurable user permissions, customizable user interfaces, support for multimedia files, and templates for defining research data representations. An evaluation of the CELO system has demonstrated its ability to efficiently create customized solutions for research laboratories with basic data management needs. The evaluation has also highlighted areas in which CELO can be improved and has elucidated potential research problems that may be of interest to the biomedical informatics field

Towards hypermedia support in database systems

The general goal of our research is to automatically generate links and other hypermedia related services to analytical applications. Using a dynamic hypermedia engine (DHE), the following features have been automated for database systems. Based on the database\u27s relational (physical) schema and its original (non-normalized) entity-relationship specification links are generated, database application developers may also specify the relationship between different classes of database elements. These elements can be controlled by the same or different database application, or even by another software system. A DHE prototype has been developed and illustrates the above for a relational database management system. The DHE is the only approach to automated linking that specializes in adding a hyperlinks automatically to analytical applications that generate their displays dynamically (e.g., as the result of a user query). The DHE\u27s linking is based on the structure of the application, not keyword search or lexical analysis based on the display values within its screens and documents. The DHE aims to provide hypermedia functionality without altering applications by building application wrappers as an intermediary between the applications and the engine