A Semantic Web approach to ontology-based system: integrating, sharing and analysing IoT health and fitness data

With the rapid development of fitness industry, Internet of Things (IoT) technology is becoming one of the most popular trends for the health and fitness areas. IoT technologies have revolutionised the fitness and the sport industry by giving users the ability to monitor their health status and keep track of their training sessions. More and more sophisticated wearable devices, fitness trackers, smart watches and health mobile applications will appear in the near future. These systems do collect data non-stop from sensors and upload them to the Cloud. However, from a data-centric perspective the landscape of IoT fitness devices and wellness appliances is characterised by a plethora of representation and serialisation formats. The high heterogeneity of IoT data representations and the lack of common accepted standards, keep data isolated within each single system, preventing users and health professionals from having an integrated view of the various information collected. Moreover, in order to fully exploit the potential of the large amounts of data, it is also necessary to enable advanced analytics over it, thus achieving actionable knowledge. Therefore, due the above situation, the aim of this thesis project is to design and implement an ontology based system to (1) allow data interoperability among heterogeneous IoT fitness and wellness devices, (2) facilitate the integration and the sharing of information and (3) enable advanced analytics over the collected data (Cognitive Computing). The novelty of the proposed solution lies in exploiting Semantic Web technologies to formally describe the meaning of the data collected by the IoT devices and define a common communication strategy for information representation and exchange

Answering SPARQL queries modulo RDF Schema with paths

SPARQL is the standard query language for RDF graphs. In its strict instantiation, it only offers querying according to the RDF semantics and would thus ignore the semantics of data expressed with respect to (RDF) schemas or (OWL) ontologies. Several extensions to SPARQL have been proposed to query RDF data modulo RDFS, i.e., interpreting the query with RDFS semantics and/or considering external ontologies. We introduce a general framework which allows for expressing query answering modulo a particular semantics in an homogeneous way. In this paper, we discuss extensions of SPARQL that use regular expressions to navigate RDF graphs and may be used to answer queries considering RDFS semantics. We also consider their embedding as extensions of SPARQL. These SPARQL extensions are interpreted within the proposed framework and their drawbacks are presented. In particular, we show that the PSPARQL query language, a strict extension of SPARQL offering transitive closure, allows for answering SPARQL queries modulo RDFS graphs with the same complexity as SPARQL through a simple transformation of the queries. We also consider languages which, in addition to paths, provide constraints. In particular, we present and compare nSPARQL and our proposal CPSPARQL. We show that CPSPARQL is expressive enough to answer full SPARQL queries modulo RDFS. Finally, we compare the expressiveness and complexity of both nSPARQL and the corresponding fragment of CPSPARQL, that we call cpSPARQL. We show that both languages have the same complexity through cpSPARQL, being a proper extension of SPARQL graph patterns, is more expressive than nSPARQL.Comment: RR-8394; alkhateeb2003

Survey over Existing Query and Transformation Languages

A widely acknowledged obstacle for realizing the vision of the Semantic Web is the inability of many current Semantic Web approaches to cope with data available in such diverging representation formalisms as XML, RDF, or Topic Maps. A common query language is the first step to allow transparent access to data in any of these formats. To further the understanding of the requirements and approaches proposed for query languages in the conventional as well as the Semantic Web, this report surveys a large number of query languages for accessing XML, RDF, or Topic Maps. This is the first systematic survey to consider query languages from all these areas. From the detailed survey of these query languages, a common classification scheme is derived that is useful for understanding and differentiating languages within and among all three areas

DTD2OWL2: A New Approach for the Transformation of the DTD to OWL

AbstractThe expansion of data sources existed in the web affects on the quality of research information. The correct answer (answer specific) of a request is all depend terms selected for their construction. Such as these terms sometimes mean more sense, the intended meaning may not be found. Fort this need, the Semantic Web has come to cover the semantic level, it proposed an ontological representation of data sources. This representation is implemented by OWL (Web Ontology Language). The current challenge of the Semantic Web is the transformation of data formats exist (SQL, XML ...) to the form of ontology (RDF, OWL ...), in order to facilitate the integration of data sources exist in the semantic web. Our target is to provide a series of extension concepts of DTD2OWL method, a simple and effective method for transforming XML documents into OWL ontologies

Implementation of a knowledge discovery and enhancement module from structured information gained from unstructured sources of information

Tese de mestrado integrado. Engenharia Informática e Computação. Faculdade de Engenharia. Universidade do Porto. 201

Formalizing Knowledge by Ontologies: OWL and KIF

During the last years, the activities of knowledge formalization and sharing useful to allow for semantically enabled management of information have been attracting growing attention, expecially in distributed environments like the Web. In this report, after a general introduction about the basis of knowledge abstraction and its formalization through ontologies, we briefly present a list of relevant formal languages used to represent knowledge: CycL, FLogic, LOOM, KIF, Ontolingua, RDF(S) and OWL. Then we focus our attention on the Web Ontology Language (OWL) and the Knowledge Interchange Format (KIF). OWL is the main language used to describe and share ontologies over the Web: there are three OWL sublanguages with a growing degree of expressiveness. We describe its structure as well as the way it is used in order to reasons over asserted knowledge. Moreover we briefly present three relevant OWL ontology editors: Prot?eg?e, SWOOP and Ontotrack and two important OWL reasoners: Pellet and FACT++. KIF is mainly a standard to describe knowledge among different computer systems so as to facilitate its exchange. We describe the main elements of KIF syntax; we also consider Sigma, an environment for creating, testing, modifying, and performing inference with KIF ontologies. We comment some meaningful example of both OWL and KIF ontologies and, in conclusion, we compare their main expresive features

Ontology based data integration in life sciences

El objetivo de la tesis es el desarrollo de una solución práctica y estándar para la integración semántica de los datos y servicios biológicos. La tesis estudia escenarios diferentes en los cuales las ontologías pueden beneficiar el desarrollo de los servicios web, su búsqueda y su visibilidad. A pesar de que las ontologías son ampliamente utilizadas en la biología, su uso habitualmente se limita a la definición de las jerarquías taxonómicas. La tesis examina la utilidad de las ontologías para la integración de los datos en el desarrollo de los servicios web semánticos. Las ontologías que definen los tipos de datos biológicos tienen un gran valor para la integración de los datos, especialmente ante un cambio continuo de los estándares. La tesis evalúa la ontología BioMoby para la generación de los servicios web conforme con las especificaciones WS-I y los servicios REST. Otro aspecto muy importante de la tesis es el uso de las ontologías para la descripción de los servicios web. La tesis evalúa la ontología WSDL promovida por el consorcio W3C para la descripción de los servicios y su búsqueda. Finalmente, se considera la integración con las plataformas modernas de la ejecución de los flujos de trabajo como Taverna y Galaxy. A pesar de la creciente popularidad del formato JSON, los servicios web dependen mucho del XML. La herramienta OWL2XS facilita el desarrollo de los servicios web semánticos generando un esquema XML a partir de una ontología OWL 2. La integración de los servicios web es difícil de conseguir sin una adaptación de los estándares. La aplicación BioNemus genera de manera automática servicios web estándar a partir de las ontologías BioMoby. La representación semántica de los servicios web simplifica su búsqueda y anotación. El Registro Semántico de Servicios Web (BioSWR) está basado en la ontología WSDL del W3C y proporciona una representación en distintos formatos: OWL 2, WSDL 1.1, WSDL 2.0 y WADL. Para demostrar los beneficios de la descripción semántica de los servicios web se ha desarrollado un plugin para Taverna. También se ha implementado una nueva librería experimental que ha sido usada en la aplicación Galaxy Gears, la cual permite la integración de los servicios web en Galaxy. La tesis explora el alcance de la aplicación de las ontologías para la integración de los datos y los servicios biológicos, proporcionando un amplio conjunto de nuevas aplicaciones.The aim of this thesis is to develop standard and practical approaches for the semantic integration of biological data and services. The thesis considers various scenarios where ontologies may benefit bioinformatics web services development, integration and provenance. In spite of the broad use of ontologies in biology, their usage is usually limited to a definition of taxonomic hierarchies. This thesis examines the utility of ontologies for data integration in context of semantic web services development. The biological datatypes ontologies are very valuable for the data integration, especially in a context of continuous standards changes. The thesis evaluates the outdated BioMoby ontology for the generation of modern WS-I and RESTful web services. Another important aspect is the use of ontologies for the web services description. The thesis evaluates the W3C standard WSDL ontology for bioinformatics web services description and provenance. Finally, the integration with modern workflow execution platforms such as Taverna and Galaxy is also considered. Despite the growing popularity of JSON format, web services vastly depend on XML type system. The OWL2XS tool facilitates semantic web services development providing the automatic XML Schema generation from an appropriate OWL 2 datatype ontology. Web services integration is hardly achievable without a broad standard adoption. The BioNemus application automatically generates standard-based web services from BioMoby ontologies. Semantic representation of web services description simplifies web services search and annotation. Semantic Web Services Registry (BioSWR) is based on W3C WSDL ontology and provides a multifaceted web services view in different formats: OWL 2, WSDL 1.1, WSDL 2.0 and WADL. To demonstrate benefits of ontology-based web services descriptions, BioSWR Taverna OSGI plug-in has been developed. The new, experimental, Taverna WSDL generic library has been used in Galaxy Gears tool which allows integrating web services into the Galaxy workflows. The thesis explores the scopes of ontologies application for the biological data and services integration, providing a broad set of original tools

Constrained regular expressions for answering RDF-path queries modulo RDFS

alkhateeb2014aInternational audienceThe standard SPARQL query language is currently defined for querying RDF graphs without RDFS semantics. Several extensions of SPARQL to RDFS semantics have been proposed. In this paper, we discuss extensions of SPARQL that use regular expressions to navigate RDF graphs and may be used to answer queries considering RDFS semantics. In particular, we present and compare nSPARQL and our proposal CPSPARQL. We show that CPSPARQL is expressive enough to answer full SPARQL queries modulo RDFS. Finally, we compare the expressiveness and complexity of both nSPARQL and the corresponding frag- ment of CPSPARQL, that we call cpSPARQL. We show that both languages have the same complexity through cpSPARQL, being a proper extension of SPARQL graph patterns, is more expressive than nSPARQL

HYDROSEEK: an ontology-aided data discovery system for hydrologic sciences

Search engines have made considerable contributions to the overall web experience. However locating scientific data remains a problem since databases are not readily accessible by search engine bots. Considering different temporal, spatial and thematic coverage of different scientific data repositories, especially for interdisciplinary research it is typically necessary to work with multiple data sources. Today integration of hydrologic data sources are mostly at the level of content aggregation by providing links to several data providers on a web page. However being able to query multiple databases simultaneously is a feature that has been sought after since the first data repositories; USGS’ National Water Information System (NWIS) and EPA’s Storage and Retrieval System (EPA STORET) came online. This study examines the current state of hydrologic data availability and dissemination in the US. It identifies the data accessibility problem and suggests a data discovery mechanism named Hydroseek as a solution. Hydroseek enables querying multiple hydrologic data repositories through a single interface and effectively combines spatial, temporal and thematic aspects of search in order to make it possible to discover more of the desired data in less time. It provides a unified view despite heterogeneity issues within and among data repositories, allows data discovery using keywords which eliminates the need to know source specific parameter codes, improves data browsing capabilities by incorporating data classification based on conceptual hierarchy and has an interface design capable of providing access to a large data inventory without overwhelming the user. System’s performance was evaluated based on statistical analysis of a user study in which users were asked to perform a certain data retrieval task using currently available systems and Hydroseek.Ph.D., Civil Engineering -- Drexel University, 200