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https://doi.org/10.21256/zhaw-18771| 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 Informatik (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 |
Dateien zu dieser Ressource:
| Datei | Beschreibung | Größe | Format | |
|---|---|---|---|---|
| SemanticQueriesOverFederatedDatabases_DatabaseJournal2019.pdf | SemanticQueriesOverFederatedDatabases_DatabaseJournal2019 | 2.27 MB | Adobe PDF |  Öffnen/Anzeigen |
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Sima, A.-C., Mendes de Farias, T., Zbinden, E., Anisimova, M., Gil, M., Stockinger, H., Stockinger, K., Robinson-Rechavi, M., & Dessimoz, C. (2019). Enabling semantic queries across federated bioinformatics databases. Database: The Journal of Biological Databases and Curation, 2019(baz106). https://doi.org/10.1093/database/baz106
Sima, A.-C. et al. (2019) ‘Enabling semantic queries across federated bioinformatics databases’, Database: The Journal of Biological Databases and Curation, 2019(baz106). Available at: https://doi.org/10.1093/database/baz106.
A.-C. Sima et al., “Enabling semantic queries across federated bioinformatics databases,” Database: The Journal of Biological Databases and Curation, vol. 2019, no. baz106, 2019, doi: 10.1093/database/baz106.
SIMA, Ana-Claudia, Tarcisio MENDES DE FARIAS, Erich ZBINDEN, Maria ANISIMOVA, Manuel GIL, Heinz STOCKINGER, Kurt STOCKINGER, Marc ROBINSON-RECHAVI und Christophe DESSIMOZ, 2019. Enabling semantic queries across federated bioinformatics databases. Database: The Journal of Biological Databases and Curation. 2019. Bd. 2019, Nr. baz106. DOI 10.1093/database/baz106
Sima, Ana-Claudia, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, and Christophe Dessimoz. 2019. “Enabling Semantic Queries across Federated Bioinformatics Databases.” Database: The Journal of Biological Databases and Curation 2019 (baz106). https://doi.org/10.1093/database/baz106.
Sima, Ana-Claudia, et al. “Enabling Semantic Queries across Federated Bioinformatics Databases.” Database: The Journal of Biological Databases and Curation, vol. 2019, no. baz106, 2019, https://doi.org/10.1093/database/baz106.
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