Brede Wiki and Brede Database 2009

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I have just drafted a section for the CIMBI 2009 annual report:

We have argued for a wiki approach to database information from published neuroimaging articles [1], and we now have implemented the Brede Wiki available from the Web site

The wiki is based on MediaWiki – the software that runs Wikipedia. With an extensive use of so-called MediaWiki templates information can be structured and easily extracted [2]. The content in the wiki is focused on neuroscience information: Text and data about neuroimaging studies, brain regions, topics, software, researchers, organizations, journals and events. The wiki makes extensive use of deep links to other neuroscience databases, enabling federation of content with other neuroinformatics databases. The Brede Wiki has almost 1,500 pages, e.g., describing 206 brain regions and 175 scientific papers. With the extracted data from the structured part of the Brede Wiki a small search interface has been constructed that allows for searching for nearby coordinates to a given query coordinate. The Brede Wiki also allows for upload of volume files in a standardized format. Thus it provides a uncomplicated means for sharing result volumes from neuroimaging statistical analyses.

Another project of the group – Brede Database – has now been included in the large scale American database federation effort ‘Neuroscience Information Framework‘. Furthermore some of the visualization efforts for the Brede Database was described in a recent article [3].

  1. Lost in localization: A solution with neuroinformatics 2.0? Finn Årup Nielsen, NeuroImage, 48:11-13, 2009
  2. Brede Wiki: Neuroscience data structured in a wiki, Finn Årup Nielsen, Proceedings of the Fourth Workshop on Semantic Wikis – The Semantic Wiki Web : 6th European Semantic Web Conference, Hersonissos, Crete, Greece, June 2009: Lange, Christoph
  3. Visualizing data mining results with the Brede tools, Finn Årup Nielsen, Frontiers in Neuroinformatics, 3:26, 2009.

The image is a figure from the CC-by Frontiers in Neuroinformatics article


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