Brede Wiki

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Brede Wiki
Category: Brede Wiki

Neuroinformatics database

Papers: DOAJ Google Scholar PubMed
Ontologies: MeSH NeuroLex Wikidata Wikipedia
Other: Google Twitter WolframAlpha

This is a graph with borders and nodes. Maybe there is an Imagemap used so the nodes may be linking to some Pages.

Brede Wiki is a wiki with structured information from neuroscience and other research areas. It contains primarily information from published peer-reviewed neuroimaging articles. It is available from

Like the Brede Database the Brede Wiki is maintained by Finn Årup Nielsen. Data from the wiki is available from

Issues raise by Rolf Kötter:[1]

Data acquisition 
Data and text can be entered with raw wiki text entry (as in Wikipedia), from SPM with Matlab script or from a Personality Genetics wiki.
Data quality control 
There is no formal quality control yet.
Data representation 
Structured data is stored with MediaWiki templates that can be exported to SQL and SKOS
System implementation 
Apache, PHP, MySQL, MediaWiki, i.e., Free and Open Source Software widespread in, e.g., Ubuntu and Debian.
User interface and documentation 
Wiki help pages and scientific publications.
Tools for data analysis 
External scripts. The Brede Toolbox may be helpful, but a direct operation is not implemented as of March 2009.
Budget and maintenance 
System is running on a computer at DTU Compute administered by Finn Årup Nielsen. Protection against vandalism may require some effort. Hopefully, readers of the wiki will turn into editors.
Legal and ethical issues 
Copyrighted and copylefted share-alike licenses. Privacy issues for researcher bibliographies. No raw imaging data.
Comparison and federation 
Extensive links to other databases where possible, XML and SQL export, MediaWiki API.
Impact and significance 
None yet (as of March 2009), since the wiki was started in January 2009.


[edit] API

The standard MediaWiki API is available for the Brede Wiki. As an example to get the frist 25 papers listed in the Papers category:


[edit] Python

[edit] Ratio of one-author papers

>>> import db
>>> bw = db.DB(filename='bredewiki-20140806-templates.sqlite3', dbtype='sqlite')
>>> df = bw.query("""select tid, count(*) as authors 
                     from brede where 
                        field="author" and 
                        (template = "paper" or 
                         template = "conference_paper")
                     group by tid""")
>>> (df.authors == 1).mean()

[edit] Papers

  1. Brede tools and federating online neuroinformatics databases
  2. Brede Wiki: a neuroinformatics Web service with structured information
  3. Brede Wiki - neuroscience data structured in a wiki
  4. Lost in localization: a solution with neuroinformatics 2.0?

[edit] Citations

  1. A framework for the collaborative specification of semantically annotated business processes
  2. Knowledge engineering for historians on the example of the catalogus professorum lipsiensis
  3. Scientific collaborations: principles of WikiBridge design

[edit] See also

[edit] References

  1. R. Kötter (2001). "Neuroscience databases: tools for exploring brain structure-function relationships". Philosophical Transactions of the Royal Society of London, Series B 356: 1111-1120. doi: 10.1098/rtsb.2001.0902.
  1. Finn Årup Nielsen(2009). "Brede Wiki: a neuroinformatics Web service with structured information". Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. doi: 10.3389/conf.neuro.11.2009.08.072. [1]
  2. Ian Johnson, Beyond bibliographies: integrating research data in a unified collaborative framework,
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