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. 2010 Dec 28:4:118.
doi: 10.3389/fninf.2010.00118. eCollection 2010.

Neuroscience Data Integration through Mediation: An (F)BIRN Case Study

Naveen Ashish  1 , José Luis Ambite, Maria Muslea, Jessica A Turner
Affiliations

Neuroscience Data Integration through Mediation: An (F)BIRN Case Study

Naveen Ashish et al. Front Neuroinform. .

Abstract

We describe an application of the BIRN mediator to the integration of neuroscience experimental data sources. The BIRN mediator is a general purpose solution to the problem of providing integrated, semantically-consistent access to biomedical data from multiple, distributed, heterogeneous data sources. The system follows the mediation approach, where the data remains at the sources, providers maintain control of the data, and the integration system retrieves data from the sources in real-time in response to client queries. Our aim with this paper is to illustrate how domain-specific data integration applications can be developed quickly and in a principled way by using our general mediation technology. We describe in detail the integration of two leading, but radically different, experimental neuroscience sources, namely, the human imaging database, a relational database, and the eXtensible neuroimaging archive toolkit, an XML web services system. We discuss the steps, sources of complexity, effort, and time required to build such applications, as well as outline directions of ongoing and future research on biomedical data integration.

Keywords: data integration; heterogeneous sources; neuroinformatics.

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Figures

Figure 1
Figure 1
Mediator architecture.
Figure 2
Figure 2
Developing a data integration application.
Figure 3
Figure 3
FBIRN query interface and results.
Figure 4
Figure 4
(Model) Heterogeneity Across HID and XNAT.
See this image and copyright information in PMC

References

    1. Adali S., Candan K. S., Papkonstantinou Y., Subrahmanian V. S. (1996). Query caching and optimization in distributed mediator systems. SIGMOD Record 25, 137–14810.1145/235968.233327 - DOI
    1. Anjomshoaa A., Antonioletti M., Atkinson M. P., Baxter R., Borley A., Chue Hong N. P., Collins B., Hardman N., Hicken G., Hume A., Knox A., Jackson M., Krause A., Laws S., Magowan J., Palansuriya C., Paton N. W., Pearson D., Sugden T., Watson P., Westhead M. (2003). The design and implementation of grid database services in OGSA-DAI. Concurrency Comput. Pract. Ex. 17, 357–376
    1. Arens Y., Knoblock C. A., Shen W.-M. (1996). Query reformulation for dynamic information integration. J. Intell. Inform. Syst. 6, 99–130
    1. Bug W. J., Ascoli G. A., Grethe J. S., Gupta A., Fennema-Notestine C., Laird A. R., Larson S. D., Rubin D., Shepherd G. M., Turner J. A., Martone M. E. (2008). The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics 6, 175–19410.1007/s12021-008-9032-z - DOI - PMC - PubMed
    1. caBIG. (2010). https://cabig.nci.nih.gov

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