neuroinformatics

Neuroinformatics coauthor network – so far

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neuroinformatics coauthor network 2016-06-28

Screenshot of neuroinformatics coauthor network – so far. Only the big cluster is shown. Network with Jonas Kress default setup querying WDQS.

Neuroinformatics databases with dia graph software

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Nielsen2011federating_database

 

So I was considering GIMP, LaTeXDraw, Inkscape, Xfig, GraphViz – and in a weak and confused movement FSLView – to draw a graph. Then I saw Dia, installed it, and I found it quite suitable. The arrows attach well to the objects and it has a range of output formats.

The unfinished graph displays neuroinformatics databases and web-linkable identifiers between them: My Brede Wiki and Brede Database along with fMRIDC, OpenfMRI, Cognitive Atlas, CogPO, IBVD, SumsDB, BODB, CoCoMac and the more general PubMed.

There is an arrow from PubMed to the Brede Database. That is because someone (not me) apparently has defined LinkOut for the Brede Database. Thank you.

Brede Wiki and Brede Database 2009

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Fninf-03-026-g010

 

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 http://neuro.imm.dtu.dk/wiki/

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

1000 total pages in the Brede Wiki

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The MediaWiki page counter for my Brede Wiki now tells me that it has passed the 1000 “total pages” mark. Pages include, e.g., comments with data on scientific articles, pages for brain regions and pages for “topics” such as neuroticism.The Brede Wiki is presently open for anonymous edits and wiki spammers are quite interested in the article on Hidehiko Takahashi. I wonder if they are communicating something via the cryptic comment fields. Disregarding the spammers the article on Richard S. J. Frackowiak seems to be the most popular article after posterior cingulate gyrus.