FishMark: A Linked Data Application Benchmark

Abstract. FishBase is an important species data collection produced by the FishBase Information and Research Group Inc (FIN), a not-forprofit NGO with the aim of collecting comprehensive information (from the taxonomic to the ecological) about all the world’s finned fish species. FishBase is exposed as a MySQL backed website (supporting a range of canned, although complex queries) and serves over 33 million hits per month. FishDelish is a transformation of FishBase into LinkedData weighing in at 1.38 billion triples. We have ported a substantial number of FishBase SQL queries to FishDelish SPARQL query which form the basis of a new linked data application benchmark (using our derivative of the Berlin SPARQL Benchmark harness). We use this benchmarking framework to compare the performance of the native MySQL application, the Virtuoso RDF triple store, and the Quest OBDA system on a fishbase.org like application.

A pragmatic approach to semantic repositories benchmarking

The aim of this paper is to benchmark various semantic repositories in order to evaluate their deployment in a commercial image retrieval and browsing application. We adopt a two-phase approach for evaluating the target semantic repositories: analytical parameters such as query language and reasoning support are used to select the pool of the target repositories, and practical parameters such as load and query response times are used to select the best match to application requirements. In addition to utilising a widely accepted benchmark for OWL repositories (UOBM), we also use a real-life dataset from the target application, which provides us with the opportunity of consolidating our findings. A distinctive advantage of this benchmarking study is that the essential requirements for the target system such as the semantic expressivity and data scalability are clearly defined, which allows us to claim contribution to the benchmarking methodology for this class of applications

Automated syntactic mediation for Web service integration

As the Web Services and Grid community adopt Semantic Web technology, we observe a shift towards higher-level workflow composition and service discovery practices. While this provides excellent functionality to non-expert users, more sophisticated middleware is required to hide the details of service invocation and service integration. An investigation of a common Bioinformatics use case reveals that the execution of high-level workflow designs requires additional processing to harmonise syntactically incompatible service interfaces. In this paper, we present an architecture to support the automatic reconciliation of data formats in such Web Service worklflows. The mediation of data is driven by ontologies that encapsulate the information contained in heterogeneous data structures supplying a common, conceptual data representation. Data conversion is carried out by a Configurable Mediator component, consuming mappings between \xml schemas and \owl ontologies. We describe our system and give examples of our mapping language against the background of a Bioinformatics use case

Using ontologies to synchronize change in relational database systems

Ontology is a building block of the semantic Web. Ontology building requires a detailed domain analysis, which in turn requires financial resources, intensive domain knowledge and time. Domain models in industry are frequently stored as relational database schemas in relational databases. An ontology base underlying such schemas can represent concepts and relationships that are present in the domain of discourse. However, with ever increasing demand for wider access and domain coverage, public databases are not static and their schemas evolve over time. Ontologies generated according to these databases have to change to reflect the new situation. Once a database schema is changed, these changes in the schema should also be incorporated in any ontology generated from the database. It is not possible to generate a fresh version of the ontology using the new database schema because the ontology itself may have undergone changes that need to be preserved. To tackle this problem, this paper presents a generic framework that will help to generate and synchronize ontologies with existing data sources. In particular we address the translation between ontologies and database schemas, but our proposal is also sufficiently generic to be used to generate and maintain ontologies based on XML and object oriented databases

An ontology-based approach to Automatic Generation of GUI for Data Entry

This thesis reports an ontology-based approach to automatic generation of highly tailored GUI components that can make customized data requests for the end users. Using this GUI generator, without knowing any programming skill a domain expert can browse the data schema through the ontology file of his/her own field, choose attribute fields according to business\u27s needs, and make a highly customized GUI for end users\u27 data requests input. The interface for the domain expert is a tree view structure that shows not only the domain taxonomy categories but also the relationships between classes. By clicking the checkbox associated with each class, the expert indicates his/her choice of the needed information. These choices are stored in a metadata document in XML. From the viewpoint of programmers, the metadata contains no ambiguity; every class in an ontology is unique. The utilizations of the metadata can be various; I have carried out the process of GUI generation. Since every class and every attribute in the class has been formally specified in the ontology, generating GUI is automatic. This approach has been applied to a use case scenario in meteorological and oceanographic (METOC) area. The resulting features of this prototype have been reported in this thesis

Annotated documents and expanded CIDOC-CRM ontology in the automatic construction of a virtual museum

The Museum of the Person (Museu da Pessoa, MP) is a virtual museum with the purpose of exhibit life stories of common people. Its assets are composed of several interviews involving people whose stories we want to perpetuate. So the museum holds an heterogeneous collection of XML (eXtensible Markup Language) documents that constitute the working repository. The main idea is to extract automatically the information included in the repository in order to build the virtual museum’s exhibition rooms. The goal of this paper is to describe an architectural approach to build a system that will create the virtual rooms from the XML repository to enable visitors to lookup individual life stories and also inter-cross information among them. We adopted the standard for museum ontologies CIDOC-CRM (CIDOC Conceptual Reference Model) refined with FOAF (Friend of a Friend) and DBpedia ontologies to represent OntoMP. That ontology is intended to allow a conceptual navigation over the available information. The approach here discussed is based on a TripleStore and uses SPARQL (SPARQL Protocol and RDF Query Language) to extract the information. Aiming at the extraction of meaningful information, we built a text filter that converts the interviews into a RDF triples file that reflects the assets described by the ontology.This work has been supported by COMPETE: POCI-01-0145-FEDER-007043 and FCT – Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/2013. The work of Ricardo Martini is supported by CNPq, grant 201772/2014-0

Utilising semantic technologies for intelligent indexing and retrieval of digital images

The proliferation of digital media has led to a huge interest in classifying and indexing media objects for generic search and usage. In particular, we are witnessing colossal growth in digital image repositories that are difficult to navigate using free-text search mechanisms, which often return inaccurate matches as they in principle rely on statistical analysis of query keyword recurrence in the image annotation or surrounding text. In this paper we present a semantically-enabled image annotation and retrieval engine that is designed to satisfy the requirements of the commercial image collections market in terms of both accuracy and efficiency of the retrieval process. Our search engine relies on methodically structured ontologies for image annotation, thus allowing for more intelligent reasoning about the image content and subsequently obtaining a more accurate set of results and a richer set of alternatives matchmaking the original query. We also show how our well-analysed and designed domain ontology contributes to the implicit expansion of user queries as well as the exploitation of lexical databases for explicit semantic-based query expansion

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

Storage of Ontology as Database and Representation of Existing Database as Ontology

Semantic Web, the next generation Web, stands out from the traditional Web by incorporating meaning to the information that is accessible to the users. Hence in effect a Web of Data is formed, represented through Ontologies. Most of the data in the traditional Web is being stored in the form of relational databases. Hence for the common man to start with ontologies, this paper tries to propose a mechanism that efficiently stores an entire ontology as a database. To move along with this transition from the traditional Web to Semantic Web, all data must be converted to a form that complies to the Semantic Web concepts. Hence this paper also proposes a mechanism to represent databases as ontology by determining the relationship between the various database components. The system proposed also tries to integrate knowledge of various databases and existing ontologies leading to a global ontology that can be used in various contexts