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

Implementing OBDA for an end-user query answering service on an educational ontology

In the age where productivity of society is no longer defined by the amount of information generated, but from the quality and assertiveness that a set of data may potentially hold, the right questions to do depends on the semantic awareness capability that an information system could evolve into. To address this challenge, in the last decade, exhaustive research has been done in the Ontology Based Data Access (OBDA) paradigm. A conspectus of the most promising technologies with data integration capabilities and the foundations where they rely are documented in this memory as a point of reference for choosing tools that supports the incorporation of a conceptual model under a OBDA method. The present study provides a practical approach for implementing an ontology based data access service, to educational context users of a Learning Analytics initiative, by means of allowing them to formulate intuitive enquiries with a familiar domain terminology on top of a Learning Management System. The ontology used was completely transformed to semantic linked data standards and some data mappings for testing were included. Semantic Linked Data technologies exposed in this document may exert modernization to environments in which object oriented and relational paradigms may propagate heterogeneous and contradictory requirements. Finally, to validate the implementation, a set of queries were constructed emulating the most relevant dynamics of the model regarding the dataset nature

Ontology-based infrastructure for intelligent applications

Ontologies currently are a hot topic in the areas of knowledge management and enterprise application integration. In this thesis, we investigate how ontologies can also be used as an infrastructure for developing applications that intelligently support a user with various tasks. Based on recent developments in the area of the Semantic Web, we provide three major contributions. We introduce inference engines, which allow the execution of business logic that is specified in a declarative way, while putting strong emphasis on scalability and ease of use. Secondly, we suggest various solutions for interfacing applications that are developed under this new paradigm with existing IT infrastructure. This includes the first running solution, to our knowledge, for combining the emerging areas of the Semantic Web Services. Finally, we introduce a set of intelligent applications, which is built on top of onologies and Semantic Web standards, providing a proof of concept that the engineering effort can largely be based on standard components.Ontologien sind derzeit ein viel diskutiertes Thema in Bereichen wie Wissensmanagement oder Enterprise Application Integration. Diese Arbeit stellt dar, wie Ontologien als Infrastruktur zur Entwicklung neuartiger Applikationen verwendet werden können, die den User bei verschiedenen Arbeiten unterstützen. Aufbauend auf den im Rahmen des Semantischen Webs entstandenen Spezifikationen, werden drei wesentliche Beiträge geleistet. Zum einen stellen wir Inferenzmaschinen vor, die das Ausführen von deklarativ spezifizierter Applikationslogik erlauben, wobei besonderes Augenmerk auf die Skalierbarkeit gelegt wird. Zum anderen schlagen wir mehrere Lösungen zum Anschluss solcher Systeme an bestehende IT Infrastruktur vor. Dies beinhaltet den, unseres Wissens nach, ersten lauffähigen Prototyp der die beiden aufstrebenden Felder des Semantischen Webs und Web Services verbindet. Schließlich stellen wir einige intelligente Applikationen vor, die auf Ontologien basieren und somit großteils von Werkzeugen automatisch generiert werden können

Exporting data from an openEHR repository to standard formats

With the healthcare sector computerization, a large amount of data is produced from medical encounters, therapeutic outcomes and other aspects of healthcare provider’s organizations current activity. Decision support systems cover several methodologies and approaches that may be applied to the healthcare sector and, since that they store and analyze data in a tabular format, it becomes necessary to assure that data sources with different data representations can be used to feed these systems. The present work focuses on the development of a methodology to export data from an openEHR repository to standard formats through a software tool which adapts itself to different data sources for later exploration in statistical and decision support systems. From use case and requirements analysis to the efective development of the tool, several steps were performed to document progress and to ground conclusions regarding operational test data. Obtained results indicate that this data export is feasible, but also highlight the need to define parameters so that the tool may function.Com a informatização do sector da saúde, uma grande quantidade de dados é produzida a partir de encontros médicos, resultados terapêuticos e outros aspectos da actividade corrente dos prestadores de cuidados. Os sistemas de apoio à decisão englobam várias metodologias e abordagens que se podem aplicar ao sector da saúde e, sendo que esses sistemas armazenam e analisam dados em formato tabular, torna-se necessário assegurar que fontes de dados com diferentes representações de informação podem ser utilizadas para alimentar estes sistemas. O presente trabalho debruça-se no desenvolvimento de uma metodologia para a exportação de dados de um repositório openEHR para formatos standard através de uma ferramenta de software que se adapte às diferentes fontes de dados para posterior análise em sistemas estatísticos e de apoio à decisão. Desde a análise de casos de uso e requerimentos até ao efectivo desenvolvimento da ferramenta, vários passos foram dados para documentar o progresso e fundamentar conclusões respeitantes aos dados dos testes operacionais. Os resultados obtidos indicam que esta exportação é exequível, mas evidenciam também a necessidade de definir parâmetros para que a ferramenta possa funcionar

Spatial ontologies for architectural heritage

Informatics and artificial intelligence have generated new requirements for digital archiving, information, and documentation. Semantic interoperability has become fundamental for the management and sharing of information. The constraints to data interpretation enable both database interoperability, for data and schemas sharing and reuse, and information retrieval in large datasets. Another challenging issue is the exploitation of automated reasoning possibilities. The solution is the use of domain ontologies as a reference for data modelling in information systems. The architectural heritage (AH) domain is considered in this thesis. The documentation in this field, particularly complex and multifaceted, is well-known to be critical for the preservation, knowledge, and promotion of the monuments. For these reasons, digital inventories, also exploiting standards and new semantic technologies, are developed by international organisations (Getty Institute, ONU, European Union). Geometric and geographic information is essential part of a monument. It is composed by a number of aspects (spatial, topological, and mereological relations; accuracy; multi-scale representation; time; etc.). Currently, geomatics permits the obtaining of very accurate and dense 3D models (possibly enriched with textures) and derived products, in both raster and vector format. Many standards were published for the geographic field or in the cultural heritage domain. However, the first ones are limited in the foreseen representation scales (the maximum is achieved by OGC CityGML), and the semantic values do not consider the full semantic richness of AH. The second ones (especially the core ontology CIDOC – CRM, the Conceptual Reference Model of the Documentation Commettee of the International Council of Museums) were employed to document museums’ objects. Even if it was recently extended to standing buildings and a spatial extension was included, the integration of complex 3D models has not yet been achieved. In this thesis, the aspects (especially spatial issues) to consider in the documentation of monuments are analysed. In the light of them, the OGC CityGML is extended for the management of AH complexity. An approach ‘from the landscape to the detail’ is used, for considering the monument in a wider system, which is essential for analysis and reasoning about such complex objects. An implementation test is conducted on a case study, preferring open source applications

Compilation and Code Optimization for Data Analytics

The trade-offs between the use of modern high-level and low-level programming languages in constructing complex software artifacts are well known. High-level languages allow for greater programmer productivity: abstraction and genericity allow for the same functionality to be implemented with significantly less code compared to low-level languages. Modularity, object-orientation, functional programming, and powerful type systems allow programmers not only to create clean abstractions and protect them from leaking, but also to define code units that are reusable and easily composable, and software architectures that are adaptable and extensible. The abstraction, succinctness, and modularity of high-level code help to avoid software bugs and facilitate debugging and maintenance. The use of high-level languages comes at a performance cost: increased indirection due to abstraction, virtualization, and interpretation, and superfluous work, particularly in the form of tempory memory allocation and deallocation to support objects and encapsulation. As a result of this, the cost of high-level languages for performance-critical systems may seem prohibitive. The vision of abstraction without regret argues that it is possible to use high-level languages for building performance-critical systems that allow for both productivity and high performance, instead of trading off the former for the latter. In this thesis, we realize this vision for building different types of data analytics systems. Our means of achieving this is by employing compilation. The goal is to compile away expensive language features -- to compile high-level code down to efficient low-level code

GENERIC AND ADAPTIVE METADATA MANAGEMENT FRAMEWORK FOR SCIENTIFIC DATA REPOSITORIES

Der rapide technologische Fortschritt hat in verschiedenen Forschungsdisziplinen zu vielfältigen Weiterentwicklungen in Datenakquise und -verarbeitung geführt. Hi- eraus wiederum resultiert ein immenses Wachstum an Daten und Metadaten, gener- iert durch wissenschaftliche Experimente. Unabhängig vom konkreten Forschungs- gebiet ist die wissenschaftliche Praxis immer stärker durch Daten und Metadaten gekennzeichnet. In der Folge intensivieren Universitäten, Forschungsgemeinschaften und Förderagenturen ihre Bemühungen, wissenschaftliche Daten effizient zu sichten, zu speichern und auszuwerten. Die wesentlichen Ziele wissenschaftlicher Daten- Repositorien sind die Etablierung von Langzeitspeicher, der Zugriff auf Daten, die Bereitstellung von Daten für die Wiederverwendung und deren Referenzierung, die Erfassung der Datenquelle zur Reproduzierbarkeit sowie die Bereitstellung von Meta- daten, Anmerkungen oder Verweisen zur Vermittlung domänenspezifischen Wis- sens, das zur Interpretation der Daten notwendig ist. Wissenschaftliche Datenspe- icher sind hochkomplexe Systeme, bestehend aus Elementen aus unterschiedlichen Forschungsfeldern, wie z. B. Algorithmen für Datenkompression und Langzeit- datenarchivierung, Frameworks für das Metadaten- und Annotations-management, Workflow-Provenance und Provenance-Interoperabilität zwischen heterogenen Work- flowsystemen, Autorisierungs und Authentifizierungsinfrastrukturen sowie Visual- isierungswerkzeuge für die Dateninterpretation. Die vorliegende Arbeit beschreibt eine modulare Architektur für ein wis- senschaftliches Datenarchiv, die Forschungsgemeinschaften darin unterstützt, ihre Daten und Metadaten gezielt über den jeweiligen Lebenszyklus hinweg zu orchestri- eren. Diese Architektur besteht aus Komponenten, die vier Forschungsfelder repräsen- tieren. Die erste Komponente ist ein Client zur Datenübertragung (“data transfer client”). Er bietet eine generische Schnittstelle für die Erfassung von Daten und den Zugriff auf Daten aus wissenschaftlichen Datenakquisesystemen. Die zweite Komponente ist das MetaStore-Framework, ein adaptives Metadaten- Management-Framework, das die Handhabung sowohl statischer als auch dynamis- cher Metadatenmodelle ermöglicht. Um beliebige Metadatenschemata behandeln zu können, basiert die Entwicklung des MetaStore-Frameworks auf dem komponen- tenbasierten dynamischen Kompositions-Entwurfsmuster (component-based dynamic composition design pattern). Der MetaStore ist außerdem mit einem Annotations- framework für die Handhabung von dynamischen Metadaten ausgestattet. Die dritte Komponente ist eine Erweiterung des MetaStore-Frameworks zur au- tomatisierten Behandlung von Provenance-Metadaten für BPEL-basierte Workflow- Management-Systeme. Der von uns entworfene und implementierte Prov2ONE Al- gorithmus übersetzt dafür die Struktur und Ausführungstraces von BPEL-Workflow- Definitionen automatisch in das Provenance-Modell ProvONE. Hierbei ermöglicht die Verfügbarkeit der vollständigen BPEL-Provenance-Daten in ProvONE nicht nur eine aggregierte Analyse der Workflow-Definition mit ihrem Ausführungstrace, sondern gewährleistet auch die Kompatibilität von Provenance-Daten aus unterschiedlichen Spezifikationssprachen. Die vierte Komponente unseres wissenschaftlichen Datenarchives ist das Provenance-Interoperabilitätsframework ProvONE - Provenance Interoperability Framework (P-PIF). Dieses gewährleistet die Interoperabilität von Provenance-Daten heterogener Provenance-Modelle aus unterschiedlichen Workflowmanagementsyste- men. P-PIF besteht aus zwei Komponenten: dem Prov2ONE-Algorithmus für SCUFL und MoML Workflow-Spezifikationen und Workflow-Management-System- spezifischen Adaptern zur Extraktion, Übersetzung und Modellierung retrospektiver Provenance-Daten in das ProvONE-Provenance-Modell. P-PIF kann sowohl Kon- trollfluss als auch Datenfluss nach ProvONE übersetzen. Die Verfügbarkeit hetero- gener Provenance-Traces in ProvONE ermöglicht das Vergleichen, Analysieren und Anfragen von Provenance-Daten aus unterschiedlichen Workflowsystemen. Wir haben die Komponenten des in dieser Arbeit vorgestellten wissenschaftlichen Datenarchives wie folgt evaluiert: für den Client zum Datentrasfer haben wir die Daten-übertragungsleistung mit dem Standard-Protokoll für Nanoskopie-Datensätze untersucht. Das MetaStore-Framework haben wir hinsichtlich der folgenden bei- den Aspekte evaluiert. Zum einen haben wir die Metadatenaufnahme und Voll- textsuchleistung unter verschiedenen Datenbankkonfigurationen getestet. Zum an- deren zeigen wir die umfassende Abdeckung der Funktionalitäten von MetaStore durch einen funktionsbasierten Vergleich von MetaStore mit bestehenden Metadaten- Management-Systemen. Für die Evaluation von P-PIF haben wir zunächst die Korrek- theit und Vollständigkeit unseres Prov2ONE-Algorithmus bewiesen und darüber hin- aus die vom Prov2ONE BPEL-Algorithmus generierten Prognose-Graphpattern aus ProvONE gegen bestehende BPEL-Kontrollflussmuster ausgewertet. Um zu zeigen, dass P-PIF ein nachhaltiges Framework ist, das sich an Standards hält, vergle- ichen wir außerdem die Funktionen von P-PIF mit denen bestehender Provenance- Interoperabilitätsframeworks. Diese Auswertungen zeigen die Überlegenheit und die Vorteile der einzelnen in dieser Arbeit entwickelten Komponenten gegenüber ex- istierenden Systemen