Original Research Article
Visualization of documents and concepts in neuroinformatics with the 3D-SE viewer
1 Laboratory for Neuroinformatics, RIKEN Brain Science Institute, Japan
2 Department of Informatics, Nicolaus Copernicus University, Poland
3 NTT Communication Science Laboratories, Japan
4 IVIS, Inc., Japan
A new interactive visualization tool is proposed for mining text data from various fields of neuroscience. Applications to several text datasets are presented to demonstrate the capability of the proposed interactive tool to visualize complex relationships between pairs of lexical entities (with some semantic contents) such as terms, keywords, posters, or papers’ abstracts. Implemented as a Java applet, this tool is based on the spherical embedding (SE) algorithm, which was designed for the visualization of bipartite graphs. Items such as words and documents are linked on the basis of occurrence relationships, which can be represented in a bipartite graph. These items are visualized by embedding the vertices of the bipartite graph on spheres in a three-dimensional (3-D) space. The main advantage of the proposed visualization tool is that 3-D layouts can convey more information than planar or linear displays of items or graphs. Different kinds of information extracted from texts, such as keywords, indexing terms, or topics are visualized, allowing interactive browsing of various fields of research featured by keywords, topics, or research teams. A typical use of the 3D-SE viewer is quick browsing of topics displayed on a sphere, then selecting one or several item(s) displays links to related terms on another sphere representing, e.g., documents or abstracts, and provides direct online access to the document source in a database, such as the Visiome Platform or the SfN Annual Meeting. Developed as a Java applet, it operates as a tool on top of existing resources.
Keywords: neuroinformatics, data visualization, bipartite graph, 3D-SE viewer, text mining, keyword extraction
Copyright: © 2007 Naud, Usui, Ueda and Taniguchi. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.
*Correspondence: Shiro Usui, Laboratory for Neuroinformatics, RIKEN Brain Science Institute, 2-1 Hirosawa,Wako City, Saitama 351-0198, Japan. e-mail: usuishiro@riken.jp
Citation: Naud A P, Usui S , Ueda N and Taniguchi T (2007) Visualization of documents and concepts in neuroinformatics with the 3D-SE viewer. Front. Neuroinform. 1:7. doi:10.3389/neuro.11.007.2007
Received: 15 September 2007; paper pending published: 09 October 2007; accepted: 16 October 2007; published online: 02 November 2007.
Edited by:
Jan G. Bjaalie, International Neuroinformatics Coordination Facility , Sweden; University of Oslo, Norway
Reviewed by:
Robert C. Cannon, Textensor Limited, UK
Gully A. Burns, USC Information Sciences Institute, USA
Gully A. Burns, USC Information Sciences Institute, USA
*Correspondence: Shiro Usui, Laboratory for Neuroinformatics, RIKEN Brain Science Institute, 2-1 Hirosawa,Wako City, Saitama 351-0198, Japan. e-mail: usuishiro@riken.jp


