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 International Journal of Web & Semantic Technology , 2012, Abstract: Increase in number of ontologies on Semantic Web and endorsement of OWL as language of discourse for the Semantic Web has lead to a scenario where research efforts in the field of ontology engineering may be applied for making the process of ontology development through reuse a viable option for ontology developers. The advantages are twofold as when existing ontological artefacts from the Semantic Web are reused, semantic heterogeneity is reduced and help in interoperability which is the essence of Semantic Web. From the perspective of ontology development advantages of reuse are in terms of cutting down on cost as well as development life as ontology engineering requires expert domain skills and is time taking process. We have devised a framework to address challenges associated with reusing ontologies from theSemantic Web. In this paper we present methods adopted for extraction and integration of concepts across multiple ontologies. We have based extraction method on features of OWL language constructs and context to extract concepts and for integration a relative semantic similarity measure is devised. We also present here guidelines for evaluation of ontology constructed. The proposed methods have been applied on concepts from food ontology and evaluation has been done on concepts from domain of academics using Golden Ontology Evaluation Method with satisfactory outcomes.
 Information Technology Journal , 2010, Abstract: The aim of this study is to develop a novel ontology ranking technique that ranks a given set of ontologies in a certain domain area. We examine each ontology by considering the OWL language constructs which are used to build that particular ontology. We define ontoweight measure and develop a methodology to compute the score and rank the ontologies. The main contributions of this study are adapting OWL constructs to determine the expressiveness of a given ontology, introducing ranking metric and methodology for ranking ontologies.
 Computer Science , 2014, DOI: 10.1186/s12859-015-0456-9 Abstract: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning. We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net.
 计算机科学 , 2008, Abstract: Ontology, ontology matching, the NBC method and OWL-S are studied in paper. OWL-S organizes resources to be services in the grid, and it expresses and describes services with service ontology, not only the semantics of service, but also the suitable inference. In view of the heterogeneity of service ontology in OWL-S, we analyze semantic match problem between ontologies, with the element values and the text of OWL and OWL-S, from the dimensions of structure, function and the text information. It has given t...
 Computer Science , 2008, Abstract: End users of recent biomedical information systems are often unaware of the storage structure and access mechanisms of the underlying data sources and can require simplified mechanisms for writing domain specific complex queries. This research aims to assist users and their applications in formulating queries without requiring complete knowledge of the information structure of underlying data sources. To achieve this, query reformulation techniques and algorithms have been developed that can interpret ontology-based search criteria and associated domain knowledge in order to reformulate a relational query. These query reformulation algorithms exploit the semantic relationships and assertion capabilities of OWL-DL based domain ontologies for query reformulation. In this paper, this approach is applied to the integrated database schema of the EU funded Health-e-Child (HeC) project with the aim of providing ontology assisted query reformulation techniques to simplify the global access that is needed to millions of medical records across the UK and Europe.
 BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-441 Abstract: We developed a method to provide definition patterns for relations between classes using OWL and describe a novel implementation of the RO based on this method. We implemented our extension in software that converts ontologies in the OBO Flatfile Format to OWL, and also provide a prototype to extract relational patterns from OWL ontologies using automated reasoning. The conversion software is freely available at http://bioonto.de/obo2owl webcite, and can be accessed via a web interface.Explicitly defining relations permits their use in reasoning software and leads to a more flexible and powerful way of representing biomedical ontologies. Using the extended langua0067e and semantics avoids several mistakes commonly made in formalizing biomedical ontologies, and can be used to automatically detect inconsistencies. The use of our method enables the use of graph-based ontologies in OWL, and makes complex OWL ontologies accessible in a graph-based form. Thereby, our method provides the means to gradually move the representation of biomedical ontologies into formal knowledge representation languages that incorporates an explicit semantics. Our method facilitates the use of OWL-based software in the back-end while ontology curators may continue to develop ontologies with an OBO-style front-end.The OBO Flatfile Format [1] is used to represent most biomedical ontologies, among them the Gene Ontology (GO) [2] and most of the OBO Foundry ontologies [3]. To achieve interoperability between ontologies of the life sciences and semantic web ontologies, a formal semantics for the OBO format is important. While several mappings from OBO to OWL exist [1,4-6], none provides a flexible representation of the OBO semantics that corresponds with the intended meaning of the ontology developers. The OBO Relationship Ontology (RO) [7] has been adopted as the reference resource for the semantics of relations within the OBO Foundry. The current mappings between OBO and OWL do not provide the m
 Olegs Verhodubs Computer Science , 2014, Abstract: This paper develops the idea of membership function assignment for OWL (Web Ontology Language) ontology elements in order to subsequently generate fuzzy rules from this ontology. The task of membership function assignment for OWL ontology elements had already been partially described, but this concerned the case, when several OWL ontologies of the same domain were available, and they were merged into a single ontology. The purpose of this paper is to present the way of membership function assignment for OWL ontology elements in the case, when there is the only one available ontology. Fuzzy rules, generated from the OWL ontology, are necessary for supplement of the SWES (Semantic Web Expert System) knowledge base. SWES is an expert system, which will be able to extract knowledge from OWL ontologies, found in the Web, and will serve as a universal expert for the user.
 Computer Science , 2014, Abstract: We investigate the size of first-order rewritings of conjunctive queries over OWL 2 QL ontologies of depth 1 and 2 by means of hypergraph programs computing Boolean functions. Both positive and negative results are obtained. Conjunctive queries over ontologies of depth 1 have polynomial-size nonrecursive datalog rewritings; tree-shaped queries have polynomial positive existential rewritings; however, in the worst case, positive existential rewritings can only be of superpolynomial size. Positive existential and nonrecursive datalog rewritings of queries over ontologies of depth 2 suffer an exponential blowup in the worst case, while first-order rewritings are superpolynomial unless $\text{NP} \subseteq \text{P}/\text{poly}$. We also analyse rewritings of tree-shaped queries over arbitrary ontologies and observe that the query entailment problem for such queries is fixed-parameter tractable.
 Computer Science , 2015, Abstract: We study confidentiality enforcement in ontologies under the Controlled Query Evaluation framework, where a policy specifies the sensitive information and a censor ensures that query answers that may compromise the policy are not returned. We focus on censors that ensure confidentiality while maximising information access, and consider both Datalog and the OWL 2 profiles as ontology languages.
 Computer Science , 2014, DOI: 10.1613/jair.3872 Abstract: The SPARQL query language is currently being extended by the World Wide Web Consortium (W3C) with so-called entailment regimes. An entailment regime defines how queries are evaluated under more expressive semantics than SPARQLs standard simple entailment, which is based on subgraph matching. The queries are very expressive since variables can occur within complex concepts and can also bind to concept or role names. In this paper, we describe a sound and complete algorithm for the OWL Direct Semantics entailment regime. We further propose several novel optimizations such as strategies for determining a good query execution order, query rewriting techniques, and show how specialized OWL reasoning tasks and the concept and role hierarchy can be used to reduce the query execution time. For determining a good execution order, we propose a cost-based model, where the costs are based on information about the instances of concepts and roles that are extracted from a model abstraction built by an OWL reasoner. We present two ordering strategies: a static and a dynamic one. For the dynamic case, we improve the performance by exploiting an individual clustering approach that allows for computing the cost functions based on one individual sample from a cluster. We provide a prototypical implementation and evaluate the efficiency of the proposed optimizations. Our experimental study shows that the static ordering usually outperforms the dynamic one when accurate statistics are available. This changes, however, when the statistics are less accurate, e.g., due to nondeterministic reasoning decisions. For queries that go beyond conjunctive instance queries we observe an improvement of up to three orders of magnitude due to the proposed optimizations.
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