Ontology-based data integration in EPNet: Production and distribution of food during the Roman Empire

Semantic technologies are rapidly changing the historical research. Over the last decades, an immense amount of new quantifiable data have been accumulated, and made available in interchangeable formats, in social sciences and humanities, opening up new possibilities for solving old questions and posing new ones. This paper introduces a framework that eases the access of scholars to historical and cultural data about food production and commercial trade system during the Roman Empire, distributed across different data sources. The proposed approach relies on the Ontology-Based Data Access (OBDA) paradigm, where the different datasets are virtually integrated by a conceptual layer (an ontology) that provides to the user a clear point of access and a unified and unambiguous conceptual view

A semantic and agent-based approach to support information retrieval, interoperability and multi-lateral viewpoints for heterogeneous environmental databases

PhDData stored in individual autonomous databases often needs to be combined and interrelated. For example, in the Inland Water (IW) environment monitoring domain, the spatial and temporal variation of measurements of different water quality indicators stored in different databases are of interest. Data from multiple data sources is more complex to combine when there is a lack of metadata in a computation forin and when the syntax and semantics of the stored data models are heterogeneous. The main types of information retrieval (IR) requirements are query transparency and data harmonisation for data interoperability and support for multiple user views. A combined Semantic Web based and Agent based distributed system framework has been developed to support the above IR requirements. It has been implemented using the Jena ontology and JADE agent toolkits. The semantic part supports the interoperability of autonomous data sources by merging their intensional data, using a Global-As-View or GAV approach, into a global semantic model, represented in DAML+OIL and in OWL. This is used to mediate between different local database views. The agent part provides the semantic services to import, align and parse semantic metadata instances, to support data mediation and to reason about data mappings during alignment. The framework has applied to support information retrieval, interoperability and multi-lateral viewpoints for four European environmental agency databases. An extended GAV approach has been developed and applied to handle queries that can be reformulated over multiple user views of the stored data. This allows users to retrieve data in a conceptualisation that is better suited to them rather than to have to understand the entire detailed global view conceptualisation. User viewpoints are derived from the global ontology or existing viewpoints of it. This has the advantage that it reduces the number of potential conceptualisations and their associated mappings to be more computationally manageable. Whereas an ad hoc framework based upon conventional distributed programming language and a rule framework could be used to support user views and adaptation to user views, a more formal framework has the benefit in that it can support reasoning about the consistency, equivalence, containment and conflict resolution when traversing data models. A preliminary formulation of the formal model has been undertaken and is based upon extending a Datalog type algebra with hierarchical, attribute and instance value operators. These operators can be applied to support compositional mapping and consistency checking of data views. The multiple viewpoint system was implemented as a Java-based application consisting of two sub-systems, one for viewpoint adaptation and management, the other for query processing and query result adjustment

Towards LLOD-based language contact studies: a case study in interoperability

We describe a methodological and technical framework for conducting qualitative and quantitative studies of linguistic research questions over diverse and heterogeneous data sources such as corpora and elicitations. We demonstrate how LLOD formalisms can be employed to develop extraction pipelines for features and linguistic examples from corpora and collections of interlinear glossed text, and furthermore, how SPARQL UPDATE can be employed (1) to normalize diverse data against a reference data model (here, POWLA), (2) to harmonize annotation vocabularies by reference to terminology repositories (here, OLiA), (3) to extract examples from these normalized data structures regardless of their origin, and (4) to implement this extraction routine in a tool-independent manner for different languages with different annotation schemes. We demonstrate our approach for language contact studies for genetically unrelated, but neighboring languages from the Caucasus area, Eastern Armenian and Georgian

Methods and Tools for Management of Distributed Event Processing Applications

Die Erfassung und Verarbeitung von Ereignissen aus cyber-physischen Systemen bietet Anwendern die Möglichkeit, kontinuierlich über Leistungsdaten und aufkommende Probleme unterrichtet zu werden (Situational Awareness) oder Wartungsprozesse zustandsabhängig zu optimieren (Condition-based Maintenance). Derartige Szenarien verlangen aufgrund der Vielzahl und Frequenz der Daten sowie der Anforderung einer echtzeitnahen Auswertung den Einsatz geeigneter Technologien. Unter dem Namen Event Processing haben sich dabei Technologien etabliert, die in der Lage sind, Datenströme in Echtzeit zu verarbeiten und komplexe Ereignismuster auf Basis räumlicher, zeitlicher oder kausaler Zusammenhänge zu erkennen. Gleichzeitig sind heute in diesem Bereich verfügbare Systeme jedoch noch durch eine hohe technische Komplexität der zugrunde liegenden deklarativen Sprachen gekennzeichnet, die bei der Entwicklung echtzeitfähiger Anwendungen zu langsamen Entwicklungszyklen aufgrund notwendiger technischer Expertise führt. Gerade diese Anwendungen weisen allerdings häufig eine hohe Dynamik in Bezug auf Veränderungen von Anforderungen der zu erkennenden Situationen, aber auch der zugrunde liegenden Sensordaten hinsichtlich ihrer Syntax und Semantik auf. Der primäre Beitrag dieser Arbeit ermöglicht Fachanwendern durch die Abstraktion von technischen Details, selbständig verteilte echtzeitfähige Anwendungen in Form von sogenannten Echtzeit-Verarbeitungspipelines zu erstellen, zu bearbeiten und auszuführen. Die Beiträge der Arbeit lassen sich wie folgt zusammenfassen: 1. Eine Methodik zur Entwicklung echtzeitfähiger Anwendungen unter Berücksichtigung von Erweiterbarkeit sowie der Zugänglichkeit für Fachanwender. 2. Modelle zur semantischen Beschreibung der Charakteristika von Ereignisproduzenten, Ereignisverarbeitungseinheiten und Ereigniskonsumenten. 3. Ein System zur Ausführung von Verarbeitungspipelines bestehend aus geographisch verteilten Ereignisverarbeitungseinheiten. 4. Ein Software-Artefakt zur graphischen Modellierung von Verarbeitungspipelines sowie deren automatisierter Ausführung. Die Beiträge werden in verschiedenen Szenarien aus den Bereichen Produktion und Logistik vorgestellt, angewendet und evaluiert

Using semantic web technologies for exploratory OLAP: A survey

Peer ReviewedPostprint (author’s final draft

Ontomet: Ontology Metadata Framework

Proper description of data, or metadata, is important to facilitate data sharing among Geospatial Information Communities. To avoid the production of arbitrary metadata annotations, communities agree that creating or adopting a metadata specification is needed. The specification is a document, such as the Geographic Metadata Standard (ISO 19115-2003), which provides a set of rules for the proper use of metadata elements. When a community is adopting a metadata specification it has two main concerns: 1) how can an existing specification be adopted, so that elements can be restricted and domain vocabularies be used? and 2) how can a metadata specification be mapped withanother one to achieve interoperability? The two aforementioned concerns are raised due to the fact that: 1) specifications lack domain-specific elements, 2) specifications have limited extensibility, 3) specifications do not always solve semantic heterogeneities and 4) methodologies to create crosswalks among specification have not been formalized. The main goal of this thesis is to present a feasible solution for these problems by providing a flexible environment to allow interoperations of formalized metadata specifications, extensions, crosswalks and domain vocabularies. The main contributions of this thesis are: 1) creation of an abstract model to represent metadata specifications, 2) development of a methodology to extend metadata specifications, called Dynamic Community Profile, and 3) formalization of semantic mappings to perform complex and contextual metadata crosswalks. These three main contributions are encapsulated in a framework called Ontology- Metadata Framework or ONTOMET. ONTOMET has seven components: metadata specification, a domain vocabulary, top-domain ontology, metadata crosswalk, Dynamic Community Profile and vocabulary mapper. A Dynamic Community Profile is a metadata specification, which extends other metadata specifications and infer terms from controlled vocabularies. Vocabulary mappers solve semantic heterogeneities that appear in domain vocabularies and a metadata crosswalk expresses the semantic mappings of two specifications. Also strategies to conceptualize metadata specifications and vocabularies, are presented. Stand alone JAVA Tools and Web programs were created that implemented the methodologies presented, to allow creation of metadata instances and mappings, as well as views of hydrologic vocabularies to facilitate discovery of knowledge and resources in the Web.Ph.D., Civil Engineering -- Drexel University, 200

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Composição de serviços para aplicações biomédicas

Doutoramento em Engenharia InformáticaA exigente inovação na área das aplicações biomédicas tem guiado a evolução das tecnologias de informação nas últimas décadas. Os desafios associados a uma gestão, integração, análise e interpretação eficientes dos dados provenientes das mais modernas tecnologias de hardware e software requerem um esforço concertado. Desde hardware para sequenciação de genes a registos electrónicos de paciente, passando por pesquisa de fármacos, a possibilidade de explorar com precisão os dados destes ambientes é vital para a compreensão da saúde humana. Esta tese engloba a discussão e o desenvolvimento de melhores estratégias informáticas para ultrapassar estes desafios, principalmente no contexto da composição de serviços, incluindo técnicas flexíveis de integração de dados, como warehousing ou federação, e técnicas avançadas de interoperabilidade, como serviços web ou LinkedData. A composição de serviços é apresentada como um ideal genérico, direcionado para a integração de dados e para a interoperabilidade de software. Relativamente a esta última, esta investigação debruçou-se sobre o campo da farmacovigilância, no contexto do projeto Europeu EU-ADR. As contribuições para este projeto, um novo standard de interoperabilidade e um motor de execução de workflows, sustentam a sucesso da EU-ADR Web Platform, uma plataforma para realizar estudos avançados de farmacovigilância. No contexto do projeto Europeu GEN2PHEN, esta investigação visou ultrapassar os desafios associados à integração de dados distribuídos e heterogéneos no campo do varíoma humano. Foi criada uma nova solução, WAVe - Web Analyses of the Variome, que fornece uma coleção rica de dados de variação genética através de uma interface Web inovadora e de uma API avançada. O desenvolvimento destas estratégias evidenciou duas oportunidades claras na área de software biomédico: melhorar o processo de implementação de software através do recurso a técnicas de desenvolvimento rápidas e aperfeiçoar a qualidade e disponibilidade dos dados através da adopção do paradigma de web semântica. A plataforma COEUS atravessa as fronteiras de integração e interoperabilidade, fornecendo metodologias para a aquisição e tradução flexíveis de dados, bem como uma camada de serviços interoperáveis para explorar semanticamente os dados agregados. Combinando as técnicas de desenvolvimento rápidas com a riqueza da perspectiva "Semantic Web in a box", a plataforma COEUS é uma aproximação pioneira, permitindo o desenvolvimento da próxima geração de aplicações biomédicas.The demand for innovation in the biomedical software domain has been an information technologies evolution driver over the last decades. The challenges associated with the effective management, integration, analyses and interpretation of the wealth of life sciences information stemming from modern hardware and software technologies require concerted efforts. From gene sequencing hardware to pharmacology research up to patient electronic health records, the ability to accurately explore data from these environments is vital to further improve our understanding of human health. This thesis encloses the discussion on building better informatics strategies to address these challenges, primarily in the context of service composition, including warehousing and federation strategies for resource integration, as well as web services or LinkedData for software interoperability. Service composition is introduced as a general principle, geared towards data integration and software interoperability. Concerning the latter, this research covers the service composition requirements within the pharmacovigilance field, namely on the European EU-ADR project. The contributions to this area, the definition of a new interoperability standard and the creation of a new workflow-wrapping engine, are behind the successful construction of the EUADR Web Platform, a workspace for delivering advanced pharmacovigilance studies. In the context of the European GEN2PHEN project, this research tackles the challenges associated with the integration of heterogeneous and distributed data in the human variome field. For this matter, a new lightweight solution was created: WAVe, Web Analysis of the Variome, provides a rich collection of genetic variation data through an innovative portal and an advanced API. The development of the strategies underlying these products highlighted clear opportunities in the biomedical software field: enhancing the software implementation process with rapid application development approaches and improving the quality and availability of data with the adoption of the Semantic Web paradigm. COEUS crosses the boundaries of integration and interoperability as it provides a framework for the flexible acquisition and translation of data into a semantic knowledge base, as well as a comprehensive set of interoperability services, from REST to LinkedData, to fully exploit gathered data semantically. By combining the lightness of rapid application development strategies with the richness of its "Semantic Web in a box" approach, COEUS is a pioneering framework to enhance the development of the next generation of biomedical applications