Rewriting Queries by Means of Model Transformations from SPARQL to OQL and Vice-Versa

Hillairet, Guillaume; Bertrand, Frédèric; Lafaye, Jean-Yves

doi:10.1007/978-3-642-02408-5_9

Cited by 7 publications

(5 citation statements)

References 8 publications

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“…We wrote a SPARQL interface to the Corvus object model which interacts directly with the Java/ORM library, taking advantage of Hibernate's ability to optimize and cache relational queries. To the best of our knowledge, although the issue of mapping SPARQL to object oriented representations such as Hibernate has been discussed [ 27 , 28 ], no tools for doing this have been released to the public. Our approach is to create wrapper classes around the Hibernate mapping classes which map the property getters to RDF predicates.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2012

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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.

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Section: Resultsmentioning

confidence: 99%

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

et al. 2012

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“…Prototypical solutions already exist in the Semantic Web community. For instance, Hillairet et al [44] use the Hibernate Query Language, an implementation of the standard Object Query Language [45] (OQL) 9 used by one of the most popular ORM vendors, to translate queries to/from SPARQL. Stadler and Lehmann [46], on the other hand, present an engine rewriting Criteria API queries to SPARQL.…”

Section: Gc4 -Object-level Query Language Related To Gc3mentioning

confidence: 99%

A comparison of object-triple mapping libraries

Ledvinka

Křemen

2020

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Domain-independent information systems like ontology editors provide only limited usability for non-experts when domain-specific linked data need to be created. On the contrary, domain-specific applications require adequate architecture for data authoring and validation, typically using the object-oriented paradigm. So far, several software libraries mapping the RDF model (representing linked data) to the object model have been introduced in the literature. In this paper, we develop a novel framework for comparison of object-triple mapping solutions in terms of features and performance. For feature comparison, we designed a set of qualitative criteria reflecting object-oriented application developer's needs. For the performance comparison, we introduce a benchmark based on a real-world information system that we implemented using one of the compared objecttriple mapping (OTM) solutions -JOPA. We present a detailed evaluation of a selected set of OTM libraries, showing how they differ in terms of features. We further narrow down the set of selected OTM libraries to contain only RDF4J-compatible ones and use the benchmark to measure their time and memory efficiency.

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“…The paper [12] aims to address query rewriting by means of model transformations. In fact, it allows querying RDF data sources via an object oriented query which is automatically rewritten in SPARQL in order to access RDF data, it also translate SPARQL queries into object oriented queries so as to implement SPARQL endpoints for object oriented applications.…”

Section: Related Workmentioning

confidence: 99%

Query Migration from Object Oriented World to Semantic World

Soussi¹,

Bahaj²

2016

IJIMAI

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-In the last decades, object-oriented approach was able to take a large share of databases market aiming to design and implement structured and reusable software through the composition of independent elements in order to have programs with a high performance. On the other hand, the mass of information stored in the web is increasing day after day with a vertiginous speed, exposing the currently web faced with the problem of creating a bridge so as to facilitate access to data between different applications and systems as well as to look for relevant and exact information wished by users. In addition, all existing approach of rewriting object oriented languages to SPARQL language rely on models transformation process to guarantee this mapping. All the previous raisons has prompted us to write this paper in order to bridge an important gap between these two heterogeneous worlds (object oriented and semantic web world) by proposing the first provably semantics preserving OQLto-SPARQL translation algorithm for each element of OQL Query (SELECT clause, FROM clause, FILTER constraint, implicit/ explicit join and union/intersection SELECT queries).

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Rewriting Queries by Means of Model Transformations from SPARQL to OQL and Vice-Versa

Cited by 7 publications

References 8 publications

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

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

A comparison of object-triple mapping libraries

Query Migration from Object Oriented World to Semantic World

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