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Publikationstyp: Beitrag in wissenschaftlicher Zeitschrift
Art der Begutachtung: Peer review (Publikation)
Titel: Enabling semantic queries across federated bioinformatics databases
Autor/-in: Sima, Ana-Claudia
Mendes de Farias, Tarcisio
Zbinden, Erich
Anisimova, Maria
Gil, Manuel
Stockinger, Heinz
Stockinger, Kurt
Robinson-Rechavi, Marc
Dessimoz, Christophe
et. al: No
DOI: 10.1093/database/baz106
10.21256/zhaw-18771
Erschienen in: Database: The Journal of Biological Databases and Curation
Band(Heft): 2019
Heft: baz106
Erscheinungsdatum: 2019
Verlag / Hrsg. Institution: Oxford University Press
ISSN: 1758-0463
Sprache: Englisch
Schlagwörter: Semantic query; Federated database; Semantic web technology; Data integration; Query processing; Natural language interface
Fachgebiet (DDC): 005: Computerprogrammierung, Programme und Daten
Zusammenfassung: Motivation: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases. Results: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface.
URI: https://digitalcollection.zhaw.ch/handle/11475/18771
Volltext Version: Publizierte Version
Lizenz (gemäss Verlagsvertrag): CC BY 4.0: Namensnennung 4.0 International
Departement: Life Sciences und Facility Management
School of Engineering
Organisationseinheit: Institut für Angewandte Informationstechnologie (InIT)
Institut für Computational Life Sciences (ICLS)
Publiziert im Rahmen des ZHAW-Projekts: Bio-SODA: Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data
Enthalten in den Sammlungen:Publikationen School of Engineering

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