Cooking the Semantic Web with the OWL API

Bechhofer, Sean; Volz, Raphael; Lord, Phillip

doi:10.1007/978-3-540-39718-2_42

Cited by 118 publications

(72 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Stage 4 and 5 of the implementation process involves a service-oriented development and deployment for the presented system architecture, as shown in Figure 6, which was used to enable the personalisation mechanism for the specified application scenario. The system was developed using Java and the OWL-API [49]. The HoD services run on the server-side, which provides the storage and usage of the Ontology model (.owl file), a set of pre-defined SWRL rules, the Reasoner, and the Application Server (Apache Tomcat).…”

Section: Methodsmentioning

confidence: 99%

Ontological user modelling and semantic rule-based reasoning for personalisation of Help-On-Demand services in pervasive environments

Skillen

Chen

Nugent

et al. 2014

Future Generation Computer Systems

View full text Add to dashboard Cite

Section: Methodsmentioning

confidence: 99%

Ontological user modelling and semantic rule-based reasoning for personalisation of Help-On-Demand services in pervasive environments

Skillen

Chen

Nugent

et al. 2014

Future Generation Computer Systems

View full text Add to dashboard Cite

“…The GO Annotation pre-processing was handled by a Java program making use of the OWLAPI OWL2 library [45] and the Pellet DL reasoner for Semantic Web data [46]. Merging of the semantic models was also handled by Java code using first the ARQ API to issue the SPARQL query on the relational Corvus store and then OWLAPI to perform the actual merge.…”

Section: Methodsmentioning

confidence: 99%

A semantic web framework to integrate cancer omics data with biological knowledge

et al. 2012

View full text Add to dashboard Cite

BackgroundThe RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge.ResultsFor this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent.ConclusionsWe were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily.

show abstract

“…The most well-known examples are JENA [24] and OWL API [25]. Since the developer works directly with the ontology-based constructs, the approach allows for flexibly using arbitrary ontologies.…”

Section: Related Workmentioning

confidence: 99%

An Architecture for Information Exchange Based on Reference Models

Paulheim

Oberle

Plendl

et al. 2012

Software Language Engineering

View full text Add to dashboard Cite

Abstract. The goal of reference models is to establish a common vocabulary and recently also to facilitate semantically unambiguous information exchange between IT systems. However, IT systems are based on implementation models that typically deviate significantly from the reference models. This raises the need for a mapping mechanism, which is flexible enough to cope with the disparities between implementation model and reference model at runtime and on instance level, and which can be implemented without altering the established IT system. We present an architecture that solves this problem by establishing methods for representing the instances of an existing IT-System in terms of a reference model. Based on rules, the concrete nature of the representation is decided at run time. Albeit our approach is entirely domain independent, we demonstrate the feasibility of our approach in an industrial case study from the Oil and Gas domain, using the ISO 15926 ontology as a reference model and mapping it to different Java and Flex implementation models.

show abstract

Cooking the Semantic Web with the OWL API

Cited by 118 publications

References 9 publications

Ontological user modelling and semantic rule-based reasoning for personalisation of Help-On-Demand services in pervasive environments

Ontological user modelling and semantic rule-based reasoning for personalisation of Help-On-Demand services in pervasive environments

A semantic web framework to integrate cancer omics data with biological knowledge

An Architecture for Information Exchange Based on Reference Models

Contact Info

Product

Resources

About