Hypermedia-based discovery for source selection using low-cost linked data interfaces

Evaluating federated Linked Data queries requires consulting multiple sources on the Web. Before a client can execute queries, it must discover data sources, and determine which ones are relevant. Federated query execution research focuses on the actual execution, while data source discovery is often marginally discussed-even though it has a strong impact on selecting sources that contribute to the query results. Therefore, the authors introduce a discovery approach for Linked Data interfaces based on hypermedia links and controls, and apply it to federated query execution with Triple Pattern Fragments. In addition, the authors identify quantitative metrics to evaluate this discovery approach. This article describes generic evaluation measures and results for their concrete approach. With low-cost data summaries as seed, interfaces to eight large real-world datasets can discover each other within 7 minutes. Hypermedia-based client-side querying shows a promising gain of up to 50% in execution time, but demands algorithms that visit a higher number of interfaces to improve result completeness

Global integration of public sector information

This paper deals with technological methods for consolidating assets lists of available public sector information (PSI) for re-use. In this direction, the effort is to review the state of the art in delivering access to PSI throughout the world and to prioritize the necessary engagements for joining available PSI catalogues. We propose an architectural framework grounded on Semantic Web technologies to deliver a global platform for federated searching. A speculative survey of available PSI portals is presented, and the initial implementation, results, and analysis of the proposed architecture are covered in detail

Coordination approaches and systems - part I : a strategic perspective

This is the first part of a two-part paper presenting a fundamental review and summary of research of design coordination and cooperation technologies. The theme of this review is aimed at the research conducted within the decision management aspect of design coordination. The focus is therefore on the strategies involved in making decisions and how these strategies are used to satisfy design requirements. The paper reviews research within collaborative and coordinated design, project and workflow management, and, task and organization models. The research reviewed has attempted to identify fundamental coordination mechanisms from different domains, however it is concluded that domain independent mechanisms need to be augmented with domain specific mechanisms to facilitate coordination. Part II is a review of design coordination from an operational perspective

A Query Integrator and Manager for the Query Web

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions

Schema architecture and their relationships to transaction processing in distributed database systems

We discuss the different types of schema architectures which could be supported by distributed database systems, making a clear distinction between logical, physical, and federated distribution. We elaborate on the additional mapping information required in architecture based on logical distribution in order to support retrieval as well as update operations. We illustrate the problems in schema integration and data integration in multidatabase systems and discuss their impact on query processing. Finally, we discuss different issues relevant to the cooperation (or noncooperation) of local database systems in a heterogeneous multidatabase system and their relationship to the schema architecture and transaction processing

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

Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and Web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases and Web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research

BlogForever D3.2: Interoperability Prospects

This report evaluates the interoperability prospects of the BlogForever platform. Therefore, existing interoperability models are reviewed, a Delphi study to identify crucial aspects for the interoperability of web archives and digital libraries is conducted, technical interoperability standards and protocols are reviewed regarding their relevance for BlogForever, a simple approach to consider interoperability in specific usage scenarios is proposed, and a tangible approach to develop a succession plan that would allow a reliable transfer of content from the current digital archive to other digital repositories is presented

Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database.

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.)