Clever generation of rich SPARQL queries from annotated relational schema: Application to Semantic Web Service creation for biological databases

Autor: Manuel Ruiz, Pierre Larmande, Julien Wollbrett, Frédéric De Lamotte
Přispěvatelé: Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Inst Biol Computat, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Region Languedoc-Roussillon, CIRAD, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Jazyk: angličtina
Rok vydání: 2013
Předmět:
0106 biological sciences
Computer science
RESOURCES
[SDV]Life Sciences [q-bio]
Interoperability
Biological database
Ontology (information science)
computer.software_genre
01 natural sciences
Biochemistry
DATA INTEGRATION
Structural Biology
Schema (psychology)
Databases
Genetic
SPARQL
0303 health sciences
Applied Mathematics
BIOINFORMATICS
000 - Autres thèmes
computer.file_format
PLANT GENOMICS
LIFE SCIENCES
CROP DATA
INTEROPERABILITY
COLLECTION
Semantics
Computer Science Applications
Vocabulary
Controlled
C30 - Documentation et information
System integration
The Internet
Web service
Algorithms
Genome
Plant
Data integration
Relational database
03 medical and health sciences
Annotation
RDF
Semantic Web
Molecular Biology
SAWSDL
030304 developmental biology
Internet
Information retrieval
business.industry
Oryza
Systems Integration
business
computer
Software
010606 plant biology & botany
Zdroj: BMC Bioinformatics
BMC Bioinformatics, BioMed Central, 2013, 14, ⟨10.1186/1471-2105-14-126⟩
BMC Bioinformatics (14), . (2013)
BMC Bioinformatics, 2013, 14, ⟨10.1186/1471-2105-14-126⟩
ISSN: 1471-2105
Popis: In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic .
Databáze: OpenAIRE
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