SHARE: A Semantic Web Query Engine for Bioinformatics

Vandervalk, Ben; McCarthy, Erin; Wilkinson, Mark D.

doi:10.1007/978-3-642-10871-6_27

Cited by 35 publications

(37 citation statements)

References 4 publications

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“…Input and output parameters are specified in terms of OWL classes. Based on the SADI recommendations, Vandervalk et al [21] present an approach to query those services with SPARQL by comparing the triple patterns of the WHERE clause with the service descriptions. Zhao et al [24] use an adaptation of SPARQL (Uniform Query) to describe Web Service interfaces as well as queries.…”

Section: Related Workmentioning

confidence: 99%

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Integrating OData services into the semantic web

Kirchhoff¹,

Geihs

2014

Proceedings of the 14th International Conference on Knowledge Technologies and Data-Driven Business

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OData is a data access protocol that allows the definition of REST-based data services. Due to the usage of standard technologies (AtomPub, HTTP and JSON), OData has gained widespread attention within the industry lately. Companies such as Microsoft and eBay provide OData interfaces for their applications and services. SAP provides OData support not only for its ERP-system but for the whole Business Suite. In order to simplify the retrieval of data from ERP-systems and to make them available for the integration with the Semantic Web, we present an approach to realize SPARQL endpoints on top of OData interfaces. The work presented in this paper mainly consists of two parts. In the first part, we define an extension of the Conceptual Schema Definition Language (CSDL) to semantically annotate OData services. In the second part, we adapt the evaluation semantics of SPARQL algebra expressions with regard to graph templates which are defined by the semantically annotated CSDL documents. Based on the adapted evaluation, we can determine the relevant OData services that need to be queried to answer a given SPARQL query. A prototypical implementation shows the feasibility of our approach.

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Section: Related Workmentioning

confidence: 99%

“…Most of these approaches aim at SOAP-/WSDL-based Web Services or RESTful services [4,24,3,11,18]. Some of them make additional constraints to the services that can be handled [22,23,21]. Angie [18] automatically enriches the local RDF knowledge base with data provided by SOAP-or RESTful services.…”

Section: Related Workmentioning

confidence: 99%

Integrating OData services into the semantic web

Kirchhoff¹,

Geihs

2014

Proceedings of the 14th International Conference on Knowledge Technologies and Data-Driven Business

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“…SADI has been employed in two well-known semantic knowledge management tools in the domain of bioinformatics, namely the IO Informatics Knowledge Explorer, and Taverna [66]. Moreover, a prototype semantic query system called SHARE (Semantic Health And Research Environment) [60] has been implemented based on SADI and the Pellet OWL-DL reasoner.…”

Section: Applicationsmentioning

confidence: 99%

Semantic Web Service Search: A Brief Survey

et al. 2015

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Scalable means for the search of relevant web services are essential for the development of intelligent service-based applications in the future Internet. Key idea of semantic web services is to enable such applications to perform a high-precision search and automated composition of services based on formal ontology-based representations of service semantics. In this paper, we briefly survey the state of the art of semantic web service search. Abstract Scalable means for the search of relevant web services are essential for the development of intelligent service-based applications in the future Internet. Key idea of semantic web services is to enable such applications to perform a high-precision search and automated composition of services based on formal ontology-based representations of service semantics. In this paper, we briefly survey the state of the art of semantic web service search.

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“…The accessible and expandable service registry of SADI helps the automated composition of computer-interpretable queries by the query engine. Use of SADI and Semantic Health and Research Environment (SHARE) [85] for scientific use cases has proven to be useful in recent literature [86,87]. Figure 2 depicts example classes from QIBO (boxes) where the direction of the arrows is from service input to service output (e.g., there is a service that returns Biological Subjects that has undergone certain Biological Interventions).…”

Section: Development Roadmapmentioning

confidence: 99%

A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers

Buckler¹,

Paik

Ouellette³

et al. 2013

J Digit Imaging

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Quantitative imaging biomarkers are of particular interest in drug development for their potential to accelerate the drug development pipeline. The lack of consensus methods and carefully characterized performance hampers the widespread availability of these quantitative measures. A framework to support collaborative work on quantitative imaging biomarkers would entail advanced statistical techniques, the development of controlled vocabularies, and a service-oriented architecture for processing large image archives. Until now, this framework has not been developed. With the availability of tools for automatic ontology-based annotation of datasets, coupled with image archives, and a means for batch selection and processing of image and clinical data, imaging will go through a similar increase in capability analogous to what advanced genetic profiling techniques have brought to molecular biology. We report on our current progress on developing an informatics infrastructure to store, query, and retrieve imaging biomarker data across a wide range of resources in a semantically meaningful way that facilitates the collaborative development and validation of potential imaging biomarkers by many stakeholders. Specifically, we describe the semantic components of our system, QI-Bench, that are used to specify and support experimental activities for statistical validation in quantitative imaging

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SHARE: A Semantic Web Query Engine for Bioinformatics

Cited by 35 publications

References 4 publications

Integrating OData services into the semantic web

Integrating OData services into the semantic web

Semantic Web Service Search: A Brief Survey

A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers

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