RODI: Benchmarking Relational-to-Ontology Mapping Generation Quality

Accessing and utilizing enterprise or Web data that is scattered across multiple data sources is an important task for both applications and users. Ontology-based data integration, where an ontology mediates between the raw data and its consumers, is a promising approach to facilitate such scenarios. This approach crucially relies on useful mappings to relate the ontology and the data, the latter being typically stored in relational databases. A number of systems to support the construction of such mappings have recently been developed. A generic and effective benchmark for reliable and comparable evaluation of the practical utility of such systems would make an important contribution to the development of ontology-based data integration systems and their application in practice. We have proposed such a benchmark, called RODI. In this paper, we present a new version of RODI, which significantly extends our previous benchmark, and we evaluate various systems with it. RODI includes test scenarios from the domains of scientific conferences, geographical data, and oil and gas exploration. Scenarios are constituted of databases, ontologies, and queries to test expected results. Systems that compute relational-to-ontology mappings can be evaluated using RODI by checking how well they can handle various features of relational schemas and ontologies, and how well the computed mappings work for query answering. Using RODI, we conducted a comprehensive evaluation of seven systems

INCMap: A Journey towards ontology-based data integration

Ontology-based data integration (OBDI) allows users to federate over heterogeneous data sources using a semantic rich conceptual data model. An important challenge in ODBI is the curation of mappings between the data sources and the global ontology. In the last years, we have built IncMap, a system to semi-automatically create mappings between relational data sources and a global ontology. IncMap has since been put into practice, both for academic and in industrial applications. Based on the experience of the last years, we have extended the original version of IncMap in several dimensions to enhance the mapping quality: (1) IncMap can detect and leverage semantic-rich patterns in the relational data sources such as inheritance for the mapping creation. (2) IncMap is able to leverage reasoning rules in the ontology to overcome structural differences from the relational data sources. (3) IncMap now includes a fully automatic mode that is often necessary to bootstrap mappings for a new data source. Our experimental evaluation shows that the new version of IncMap outperforms its previous version as well as other state-of-the-art systems

Generating Data Wrapping Ontologies from Sensor Networks: a case study

Information coming from sensor networks is being increasingly used in a variety of systems (decision support systems, information portals, etc), normally combined with information coming from more traditional sources (e.g., relational databases, web documents, etc). However, existing ontology based information integration approaches cannot be easily used for this combination task since they are mainly focused on the integration of information coming from these traditional sources, and do not support sensor network data. In this paper we make a first step towards enabling the inclusion of sensor network data into these integration approaches, with the automatic generation of data wrapping ontologies for sensor networks. Our approach extends existing ones used for extracting data wrapping ontologies from relational databases, using the schema of sensor network queries and external ontology search and relation discovery services

Enabling semantic queries across federated bioinformatics databases

MOTIVATION: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases. RESULTS: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface

Methods and techniques for generation and integration of Web ontology data

University of Technology, Sydney. Faculty of Information Technology.Data integration over the web or across organizations encounters several unfavorable features: heterogeneity, decentralization, incompleteness, and uncertainty, which prevent information from being fully utilized for advanced applications such as decision support services. The basic idea of ontology related approaches for data integration is to use one or more ontology schemas to interpret data from different sources. Several issues will come up when actually implementing the idea: (1) How to develop the domain ontology schema(s) used for the integration; (2) How to generate ontology data for domain ontology schema if the data are not in the right format and to create and manage ontology data in an appropriate way; (3) How to improve the quality of integrated ontology data by reducing duplications and increasing completeness and certainty. This thesis focuses on the above issues and develops a set of methods to tackle them. First, a key information mining method is developed to facilitate the development of interested domain ontology schemas. It effectively extracts from the web sites useful terms and identifies taxonomy information which is essential to ontology schema construction. A prototype system is developed to use this method to help create domain ontology schemas. Second, this study develops two complemented methods which are light weighted and more semantic web oriented to address the issue of ontology data generation. One method allows users to convert existing structured data (mostly XML data) to ontology data; another enables users to create new ontology data directly with ease.In addition, a web-based system is developed to allow users to manage the ontology data collaboratively and with customizable security constraints. Third, this study also proposes two methods to perform ontology data matching for the improvement of ontology data quality when an integration happens. One method uses the clustering approach. It makes use of the relational nature of the ontology data and captures different situations of matching, therefore resulting in an improvement of performance compared with the traditional canopy clustering method. The other method goes further by using a learning mechanism to make the matching more adaptive. New features are developed for training matching classifier by exploring particular characteristics of ontology data. This method also achieves better performance than those with only ordinary features. These matching methods can be used to improve data quality in a peer-to-peer framework which is proposed to integrate available ontology data from different peers

Virtual Knowledge Graphs: An Overview of Systems and Use Cases

In this paper, we present the virtual knowledge graph (VKG) paradigm for data integration and access, also known in the literature as Ontology-based Data Access. Instead of structuring the integration layer as a collection of relational tables, the VKG paradigm replaces the rigid structure of tables with the flexibility of graphs that are kept virtual and embed domain knowledge. We explain the main notions of this paradigm, its tooling ecosystem and significant use cases in a wide range of applications. Finally, we discuss future research directions

A Shared Ontology Approach to Semantic Representation of BIM Data

Architecture, engineering, construction and facility management (AEC-FM) projects involve a large number of participants that must exchange information and combine their knowledge for successful completion of a project. Currently, most of the AEC-FM domains store their information about a project in text documents or use XML, relational, or object-oriented formats that make information integration difficult. The AEC-FM industry is not taking advantage of the full potential of the Semantic Web for streamlining sharing, connecting, and combining information from different domains. The Semantic Web is designed to solve the information integration problem by creating a web of structured and connected data that can be processed by machines. It allows combining information from different sources with different underlying schemas distributed over the Internet. In the Semantic Web, all data instances and data schema are stored in a graph data store, which makes it easy to merge data from different sources. This paper presents a shared ontology approach to semantic representation of building information. The semantic representation of building information facilitates finding and integrating building information distributed in several knowledge bases. A case study demonstrates the development of a semantic based building design knowledge base

On the Foundations of Data Interoperability and Semantic Search on the Web

This dissertation studies the problem of facilitating semantic search across disparate ontologies that are developed by different organizations. There is tremendous potential in enabling users to search independent ontologies and discover knowledge in a serendipitous fashion, i.e., often completely unintended by the developers of the ontologies. The main difficulty with such search is that users generally do not have any control over the naming conventions and content of the ontologies. Thus terms must be appropriately mapped across ontologies based on their meaning. The meaning-based search of data is referred to as semantic search, and its facilitation (aka semantic interoperability) then requires mapping between ontologies. In relational databases, searching across organizational boundaries currently involves the difficult task of setting up a rigid information integration system. Linked Data representations more flexibly tackle the problem of searching across organizational boundaries on the Web. However, there exists no consensus on how ontology mapping should be performed for this scenario, and the problem is open. We lay out the foundations of semantic search on the Web of Data by comparing it to keyword search in the relational model and by providing effective mechanisms to facilitate data interoperability across organizational boundaries. We identify two sharply distinct goals for ontology mapping based on real-world use cases. These goals are: (i) ontology development, and (ii) facilitating interoperability. We systematically analyze these goals, side-by-side, and contrast them. Our analysis demonstrates the implications of the goals on how to perform ontology mapping and how to represent the mappings. We rigorously compare facilitating interoperability between ontologies to information integration in databases. Based on the comparison, class matching is emphasized as a critical part of facilitating interoperability. For class matching, various class similarity metrics are formalized and an algorithm that utilizes these metrics is designed. We also experimentally evaluate the effectiveness of the class similarity metrics on real-world ontologies. In order to encode the correspondences between ontologies for interoperability, we develop a novel W3C-compliant representation, named skeleton