A survey of RDB to RDF translation approaches and tools

ISRN I3S/RR 2013-04-FR 24 pagesRelational databases scattered over the web are generally opaque to regular web crawling tools. To address this concern, many RDB-to-RDF approaches have been proposed over the last years. In this paper, we propose a detailed review of seventeen RDB-to-RDF initiatives, considering end-to-end projects that delivered operational tools. The different tools are classified along three major axes: mapping description language, mapping implementation and data retrieval method. We analyse the motivations, commonalities and differences between existing approaches. The expressiveness of existing mapping languages is not always sufficient to produce semantically rich data and make it usable, interoperable and linkable. We therefore briefly present various strategies investigated in the literature to produce additional knowledge. Finally, we show that R2RML, the W3C recommendation for describing RDB to RDF mappings, may not apply to all needs in the wide scope of RDB to RDF translation applications, leaving space for future extensions

An Algorithm for Inferring Big Data Objects Correlation Using Word Net

© 2016 The Authors. The value of big data comes from its variety where data is collected from various sources. One of the key big data challenges is identifying which data objects are relevant or refer to the same logical entity across various data sources. This challenge is traditionally known as schema matching. Due to big data velocity traditional approaches to data matching can no longer be used. In this paper we present an approach for inferring data objects correlation. We present our algorithm that relies on the objects meta-data and it consults the Word Net thesaurus

A survey of RDB to RDF translation approaches and tools

ISRN I3S/RR 2013-04-FR 24 pagesRelational databases scattered over the web are generally opaque to regular web crawling tools. To address this concern, many RDB-to-RDF approaches have been proposed over the last years. In this paper, we propose a detailed review of seventeen RDB-to-RDF initiatives, considering end-to-end projects that delivered operational tools. The different tools are classified along three major axes: mapping description language, mapping implementation and data retrieval method. We analyse the motivations, commonalities and differences between existing approaches. The expressiveness of existing mapping languages is not always sufficient to produce semantically rich data and make it usable, interoperable and linkable. We therefore briefly present various strategies investigated in the literature to produce additional knowledge. Finally, we show that R2RML, the W3C recommendation for describing RDB to RDF mappings, may not apply to all needs in the wide scope of RDB to RDF translation applications, leaving space for future extensions

Enabling Complex Semantic Queries to Bioinformatics Databases through Intuitive Search Over Data

Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data already available publicly. However, the heterogene- ity of the existing data sources still poses significant challenges for achieving interoperability among biological databases. Furthermore, merely solving the technical challenges of data in- tegration, for example through the use of common data representation formats, leaves open the larger problem. Namely, the steep learning curve required for understanding the data models of each public source, as well as the technical language through which the sources can be queried and joined. As a consequence, most of the available biological data remain practically unexplored today. In this thesis, we address these problems jointly, by first introducing an ontology-based data integration solution in order to mitigate the data source heterogeneity problem. We illustrate through the concrete example of Bgee, a gene expression data source, how relational databases can be exposed as virtual Resource Description Framework (RDF) graphs, through relational-to-RDF mappings. This has the important advantage that the original data source can remain unmodified, while still becoming interoperable with external RDF sources. We complement our methods with applied case studies designed to guide domain experts in formulating expressive federated queries targeting the integrated data across the domains of evolutionary relationships and gene expression. More precisely, we introduce two com- parative analyses, first within the same domain (using orthology data from multiple, inter- operable, data sources) and second across domains, in order to study the relation between expression change and evolution rate following a duplication event. Finally, in order to bridge the semantic gap between users and data, we design and im- plement Bio-SODA, a question answering system over domain knowledge graphs, that does not require training data for translating user questions to SPARQL. Bio-SODA uses a novel ranking approach that combines syntactic and semantic similarity, while also incorporating node centrality metrics to rank candidate matches for a given user question. Our results in testing Bio-SODA across several real-world databases that span multiple domains (both within and outside bioinformatics) show that it can answer complex, multi-fact queries, be- yond the current state-of-the-art in the more well-studied open-domain question answering. -- L’intégration des données promet d’être l’un des principaux catalyseurs permettant d’extraire des nouveaux aperçus de la richesse des données biologiques déjà disponibles publiquement. Cependant, l’hétérogénéité des sources de données existantes pose encore des défis importants pour parvenir à l’interopérabilité des bases de données biologiques. De plus, en surmontant seulement les défis techniques de l’intégration des données, par exemple grâce à l’utilisation de formats standard de représentation de données, on laisse ouvert un problème encore plus grand. À savoir, la courbe d’apprentissage abrupte nécessaire pour comprendre la modéli- sation des données choisie par chaque source publique, ainsi que le langage technique par lequel les sources peuvent être interrogés et jointes. Par conséquent, la plupart des données biologiques publiquement disponibles restent pratiquement inexplorés aujourd’hui. Dans cette thèse, nous abordons l’ensemble des deux problèmes, en introduisant d’abord une solution d’intégration de données basée sur ontologies, afin d’atténuer le problème d’hété- rogénéité des sources de données. Nous montrons, à travers l’exemple de Bgee, une base de données d’expression de gènes, une approche permettant les bases de données relationnelles d’être publiés sous forme de graphes RDF (Resource Description Framework) virtuels, via des correspondances relationnel-vers-RDF (« relational-to-RDF mappings »). Cela présente l’important avantage que la source de données d’origine peut rester inchangé, tout en de- venant interopérable avec les sources RDF externes. Nous complétons nos méthodes avec des études de cas appliquées, conçues pour guider les experts du domaine dans la formulation de requêtes fédérées expressives, ciblant les don- nées intégrées dans les domaines des relations évolutionnaires et de l’expression des gènes. Plus précisément, nous introduisons deux analyses comparatives, d’abord dans le même do- maine (en utilisant des données d’orthologie provenant de plusieurs sources de données in- teropérables) et ensuite à travers des domaines interconnectés, afin d’étudier la relation entre le changement d’expression et le taux d’évolution suite à une duplication de gène. Enfin, afin de mitiger le décalage sémantique entre les utilisateurs et les données, nous concevons et implémentons Bio-SODA, un système de réponse aux questions sur des graphes de connaissances domaine-spécifique, qui ne nécessite pas de données de formation pour traduire les questions des utilisateurs vers SPARQL. Bio-SODA utilise une nouvelle ap- proche de classement qui combine la similarité syntactique et sémantique, tout en incorporant des métriques de centralité des nœuds, pour classer les possibles candidats en réponse à une question utilisateur donnée. Nos résultats suite aux tests effectués en utilisant Bio-SODA sur plusieurs bases de données à travers plusieurs domaines (tantôt liés à la bioinformatique qu’extérieurs) montrent que Bio-SODA réussit à répondre à des questions complexes, en- gendrant multiples entités, au-delà de l’état actuel de la technique en matière de systèmes de réponses aux questions sur les données structures, en particulier graphes de connaissances

Constructing data marts from web sources using a graph common model

At a time when humans and devices are generating more information than ever, activities such as data mining and machine learning become crucial. These activities enable us to understand and interpret the information we have and predict, or better prepare ourselves for, future events. However, activities such as data mining cannot be performed without a layer of data management to clean, integrate, process and make available the necessary datasets. To that extent, large and costly data flow processes such as Extract-Transform-Load are necessary to extract from disparate information sources to generate ready-for-analyses datasets. These datasets are generally in the form of multi-dimensional cubes from which different data views can be extracted for the purpose of different analyses. The process of creating a multi-dimensional cube from integrated data sources is significant. In this research, we present a methodology to generate these cubes automatically or in some cases, close to automatic, requiring very little user interaction. A construct called a StarGraph acts as a canonical model for our system, to which imported data sources are transformed. An ontology-driven process controls the integration of StarGraph schemas and simple OLAP style functions generate the cubes or datasets. An extensive evaluation is carried out using a large number of agri data sources with user-defined case studies to identify sources for integration and the types of analyses required for the final data cubes

An object query language for multimedia federations

The Fischlar system provides a large centralised repository of multimedia files. As expansion is difficult in centralised systems and as different user groups have a requirement to define their own schemas, the EGTV (Efficient Global Transactions for Video) project was established to examine how the distribution of this database could be managed. The federated database approach is advocated where global schema is designed in a top-down approach, while all multimedia and textual data is stored in object-oriented (O-O) and object-relational (0-R) compliant databases. This thesis investigates queries and updates on large multimedia collections organised in the database federation. The goal of this research is to provide a generic query language capable of interrogating global and local multimedia database schemas. Therefore, a new query language EQL is defined to facilitate the querying of object-oriented and objectrelational database schemas in a database and platform independent manner, and acts as a canonical language for database federations. A new canonical language was required as the existing query language standards (SQL: 1999 and OQL) axe generally incompatible and translation between them is not trivial. EQL is supported with a formally defined object algebra and specified semantics for query evaluation. The ability to capture and store metadata of multiple database schemas is essential when constructing and querying a federated schema. Therefore we also present a new platform independent metamodel for specifying multimedia schemas stored in both object-oriented and object-relational databases. This metadata information is later used for the construction of a global schemas, and during the evaluation of local and global queries. Another important feature of any federated system is the ability to unambiguously define database schemas. The schema definition language for an EGTV database federation must be capable of specifying both object-oriented and object-relational schemas in the database independent format. As XML represents a standard for encoding and distributing data across various platforms, a language based upon XML has been developed as a part of our research. The ODLx (Object Definition Language XML) language specifies a set of XMLbased structures for defining complex database schemas capable of representing different multimedia types. The language is fully integrated with the EGTV metamodel through which ODLx schemas can be mapped to 0-0 and 0-R databases

Representing and integrating bibliographic information into the Semantic Web : A comparison of four conceptual models

Integration of library data into the Semantic Web environment is a key issue for libraries and is approached on the basis of interoper- ability between conceptual models. Several data models exist for the representation and publication of library data in the Semantic Web and therefore inter-domain and intra-domain interoperability issues emerge as a growing number of web data are generated. Achieving interoperability for different representations of the same or related entities between the library and other cultural heritage institutions shall enhance rich bibliographic data reusability and support the development of new data-driven information services. This paper aims to investigate common ground and convergences between four conceptual models, namely Functional Requirements for Bibliographic Records (FRBR), FRBR Object-Oriented (FRBRoo), Bibliographic Framework (BIBFRAME) and Europeana Data Model (EDM), enabling semantically-richer interoperability by studying the representation of monographs, as well as of content relationships (derivative and equivalent bibliographic relationships) and of whole-part relationships between them

Flexible Integration and Efficient Analysis of Multidimensional Datasets from the Web

If numeric data from the Web are brought together, natural scientists can compare climate measurements with estimations, financial analysts can evaluate companies based on balance sheets and daily stock market values, and citizens can explore the GDP per capita from several data sources. However, heterogeneities and size of data remain a problem. This work presents methods to query a uniform view - the Global Cube - of available datasets from the Web and builds on Linked Data query approaches

The XFM view adaptation mechanism: An essential component for XML data warehouses

In the past few years, with many organisations providing web services for business and communication purposes, large volumes of XML transactions take place on a daily basis. In many cases, organisations maintain these transactions in their native XML format due to its flexibility for xchanging data between heterogeneous systems. This XML data provides an important resource for decision support systems. As a consequence, XML technology has slowly been included within decision support systems of data warehouse systems. The problem encountered is that existing native XML database systems suffer from poor performance in terms of managing data volume and response time for complex analytical queries. Although materialised XML views can be used to improve the performance for XML data warehouses, update problems then become the bottleneck of using materialised views. Specifically, synchronising materialised views in the face of changing view definitions, remains a significant issue. In this dissertation, we provide a method for XML-based data warehouses to manage updates caused by the change of view definitions (view redefinitions), which is referred to as the view adaptation problem. In our approach, views are defined using XPath and then modelled using a set of novel algebraic operators and fragments. XPath views are integrated into a single view graph called the XML Fragment Materialisation (XFM) View Graph, where common parts between different views are shared and appear only once in the graph. Fragments within the view graph can be selected for materialisation to facilitate the view adaptation process. While changes are applied, our view adaptation algorithms can quickly determine what part of the XFM view graph is affected. The adaptation algorithms then perform a structural adaptation to update the view graph, followed by data adaptation to update materialised fragments

Open City Data Pipeline

Statistical data about cities, regions and at country level is collected for various purposes and from various institutions. Yet, while access to high quality and recent such data is crucial both for decision makers as well as for the public, all to often such collections of data remain isolated and not re-usable, let alone properly integrated. In this paper we present the Open City Data Pipeline, a focused attempt to collect, integrate, and enrich statistical data collected at city level worldwide, and republish this data in a reusable manner as Linked Data. The main feature of the Open City Data Pipeline are: (i) we integrate and cleanse data from several sources in a modular and extensible, always up-to-date fashion; (ii) we use both Machine Learning techniques as well as ontological reasoning over equational background knowledge to enrich the data by imputing missing values, (iii) we assess the estimated accuracy of such imputations per indicator. Additionally, (iv) we make the integrated and enriched data available both in a we browser interface and as machine-readable Linked Data, using standard vocabularies such as QB and PROV, and linking to e.g. DBpedia. Lastly, in an exhaustive evaluation of our approach, we compare our enrichment and cleansing techniques to a preliminary version of the Open City Data Pipeline presented at ISWC2015: firstly, we demonstrate that the combination of equational knowledge and standard machine learning techniques significantly helps to improve the quality of our missing value imputations; secondly, we arguable show that the more data we integrate, the more reliable our predictions become. Hence, over time, the Open City Data Pipeline shall provide a sustainable effort to serve Linked Data about cities in increasing quality.Series: Working Papers on Information Systems, Information Business and Operation