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Infrastructure for Neuroscience Ontologies Bridging Between Experimental Data in 3D Atlas, Computational Modeling and Analytical Tools: A basement Approach of DynamicBrain Platform (DB-PF) toward Inter-Platform Coordination in the J-Node

Hiroaki Wagatsuma1, 2*, Yoshiyuki Asai3 and Taishin Nomura4
  • 1 Kyushu Institute of Technology, Graduate School of Life Science and Systems Engineering, Japan
  • 2 RIKEN Brain Science Institute, Japan
  • 3 Okinawa Institute of Science and Technology, Japan
  • 4 Osaka University, Department of Mechanical Science and Bioengineering, Japan

Neuroscience ontologies have been discussed energetically in the International Neuroinformatics Coordinating Facility (INCF) and related international nodes [1]. Ontologies in general is convenient for readers who are interested in items of the database or website, offering sophisticated accesses based on the Web Ontology Language (OWL) [2] to increase accessibility. Neuroinformatics platforms of the INCF Japan-Node are organized in the XooNIps system [3], which needs to design an additional module to access with OWL based queries like a form that Linked Open Data (LOD) offers [4]. For example, a J-Node platform, ViBrism (Virtual Brain with 3D-ISM) is a 3D-map database of endogenous gene expression in a virtual whole mouse brain produced with an original sampling-device [5], which is expected to connect to other J-Node platforms effectively. We DynamicBrain Platform (DB-PF) have cooperated with Physiome.jp [6], which is a part of the Worldwide Integrative Biomedical Research Cooperation to promote Physiome and Systems Biology and organize the PHML Model Database, and PhysioDesigner and Garuda alliance [7], which is an open platform that supports multilevel modeling of physiological systems in the field of integrated life sciences and systems biology including physiology and neuroscience. In this approach, we tried to connect between the XooNIps database and PHML Model Database by using a Java client application, as the preparation to link between the 3D-map database such as ViBrism and XooNIps model database. A code to represent 3D positions and supplemental information on the linked data is possible to embed into the description property of the XooNIps database, which enhances a potential of the current XooNIps and provides an opportunity to consider on the next generation and possible cross communications in J-Node platforms.

Acknowledgements

This work was partly supported by Neuroinformatics Japan Center and RIKEN Brain Science Institute.

References

[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, doi: 10.1007/s12021-008-9032-z.
[2] Lam, H. Y., Marenco, L., Shepherd, G. M., Miller, P. L., Cheung, K. H. (2006) Using web ontology language to integrate heterogeneous databases in the neurosciences, AMIA Annu Symp Proc. 2006:464-468.
[3] XooNIps Official Site, http://xoonips.osdn.jp
[4] TaskForces/CommunityProjects/LinkingOpenData/DataSets, http://www.w3.org/wiki/TaskForces/CommunityProjects/LinkingOpenData/DataSets
[5] ViBrism: a database of comprehensive gene expression maps produced with Transcriptome Tomography, http://vibrism.neuroinf.jp
[6] Physiome and Systems Biology, http://www.physiome.jp
[7] PhysioDesigner, http://www.physiodesigner.org

Keywords: Web Ontology Language (OWL), Linked Open Data (LOD), 3D-map database, XooNIps, Physiome.jp, PhysioDesigner, Garuda alliance, ViBrism

Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.

Presentation Type: Poster, to be considered for oral presentation

Topic: Infrastructural and portal services

Citation: Wagatsuma H, Asai Y and Nomura T (2015). Infrastructure for Neuroscience Ontologies Bridging Between Experimental Data in 3D Atlas, Computational Modeling and Analytical Tools: A basement Approach of DynamicBrain Platform (DB-PF) toward Inter-Platform Coordination in the J-Node. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00049

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Received: 31 May 2015; Published Online: 05 Aug 2015.

* Correspondence: Prof. Hiroaki Wagatsuma, Kyushu Institute of Technology, Graduate School of Life Science and Systems Engineering, Fukuoka, Fukuoka 808-0196, Japan, waga@brain.kyutech.ac.jp