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Methods ARTICLE

Visualizing data mining results with the Brede tools

Finn Årup Nielsen1,2,3*
1
Center for Integrated Molecular Brain Imaging, Copenhagen, Denmark
2
DTU Informatics, Technical University of Denmark, Lyngby, Denmark
3
Neurobiology Research Unit, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
A few neuroinformatics databases now exist that record results from neuroimaging studies in the form of brain coordinates in stereotaxic space. The Brede Toolbox was originally developed to extract, analyze and visualize data from one of them – the BrainMap database. Since then the Brede Toolbox has expanded and now includes its own database with coordinates along with ontologies for brain regions and functions: The Brede Database. With Brede Toolbox and Database combined, we setup automated workflows for extraction of data, mass meta-analytic data mining and visualizations. Most of the Web presence of the Brede Database is established by a single script executing a workflow involving these steps together with a final generation of Web pages with embedded visualizations and links to interactive three-dimensional models in the Virtual Reality Modeling Language. Apart from the Brede tools I briefly review alternate visualization tools and methods for Internet-based visualization and information visualization as well as portals for visualization tools.
Keywords:
neuroimaging, visualization, software, meta-analysis, database, text mining, Web service, Brede
Citation:
Nielsen FA (2009). Visualizing data mining results with the Brede tools. Front. Neuroinform. 3:26. doi: 10.3389/neuro.11.026.2009
Received:
01 April 2009;
 Paper pending published:
01 May 2009;
Accepted:
10 July 2009;
 Published online:
28 July 2009.

Edited by:

John Van Horn, University of California at Los Angeles, USA

Reviewed by:

Kate Fissell, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
John Van Horn, University of California, Los Angeles, CA, USA
Copyright:
© 2009 Nielsen. 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:
Finn Årup Nielsen, DTU Informatics, Richard Petersens Plads, DTU, 2800 Kongens Lyngby, Denmark. e-mail: fn@imm.dtu.dk

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