Ontology-Based Data Access and Integration

An ontology-based data integration (OBDI) system is an information management system consisting of three components: an ontology, a set of data sources, and the mapping between the two. The ontology is a conceptual, formal description of the domain of interest to a given organization (or a community of users), expressed in terms of relevant concepts, attributes of concepts, relationships between concepts, and logical assertions characterizing the domain knowledge. The data sources are the repositories accessible by the organization where data concerning the domain are stored. In the general case, such repositories are numerous, heterogeneous, each one managed and maintained independently from the others. The mapping is a precise specification of the correspondence between the data contained in the data sources and the elements of the ontology. The main purpose of an OBDI system is to allow information consumers to query the data using the elements in the ontology as predicates. In the special case where the organization manages a single data source, the term ontology-based data access (ODBA) system is used

Using Ontologies for Semantic Data Integration

While big data analytics is considered as one of the most important paths to competitive advantage of today’s enterprises, data scientists spend a comparatively large amount of time in the data preparation and data integration phase of a big data project. This shows that data integration is still a major challenge in IT applications. Over the past two decades, the idea of using semantics for data integration has become increasingly crucial, and has received much attention in the AI, database, web, and data mining communities. Here, we focus on a specific paradigm for semantic data integration, called Ontology-Based Data Access (OBDA). The goal of this paper is to provide an overview of OBDA, pointing out both the techniques that are at the basis of the paradigm, and the main challenges that remain to be addressed

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

Functional Ontologies and Their Application to Hydrologic Modeling: Development of an Integrated Semantic and Procedural Knowledge Model and Reasoning Engine

This dissertation represents the research and development of new concepts and techniques for modeling the knowledge about the many concepts we as hydrologists must understand such that we can execute models that operate in terms of conceptual abstractions and have those abstractions translate to the data, tools, and models we use every day. This hydrologic knowledge includes conceptual (i.e. semantic) knowledge, such as the hydrologic cycle concepts and relationships, as well as functional (i.e. procedural) knowledge, such as how to compute the area of a watershed polygon, average basin slope or topographic wetness index. This dissertation is presented as three papers and a reference manual for the software created. Because hydrologic knowledge includes both semantic aspects as well as procedural aspects, we have developed, in the first paper, a new form of reasoning engine and knowledge base that extends the general-purpose analysis and problem-solving capability of reasoning engines by incorporating procedural knowledge, represented as computer source code, into the knowledge base. The reasoning engine is able to compile the code and then, if need be, execute the procedural code as part of a query. The potential advantage to this approach is that it simplifies the description of procedural knowledge in a form that can be readily utilized by the reasoning engine to answer a query. Further, since the form of representation of the procedural knowledge is source code, the procedural knowledge has the full capabilities of the underlying language. We use the term functional ontology to refer to the new semantic and procedural knowledge models. The first paper applies the new knowledge model to describing and analyzing polygons. The second and third papers address the application of the new functional ontology reasoning engine and knowledge model to hydrologic applications. The second paper models concepts and procedures, including running external software, related to watershed delineation. The third paper models a project scenario that includes integrating several models. A key advance demonstrated in this paper is the use of functional ontologies to apply metamodeling concepts in a manner that both abstracts and fully utilizes computational models and data sets as part of the project modeling process

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