Brede Database

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Brede Database
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Category: Brede Database
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Brede Database is a neuroinformatics database with results from published neuroimaging studies. It features search on Talairach coordinates. It is available from

http://neuro.compute.dtu.dk/services/brededatabase/

Functions from the Brede Toolbox are able to read data associated with the Brede Database. The XML files of the Brede Database are also distributed along with the Brede Toolbox. Papers in the Brede Wiki that is also listed in the Brede Database is recorded in the Papers in Brede Database category.

The different forms of visualizations construct on the Web pages of the Brede Database are described in Visualizing data mining results with the Brede tools.[1] The database was introduced in a abstract for the Human Brain Mapping conference.[2]

Parts of the Brede Database are federated into the Web database service provided by the Neuroscience Information Framework.

It is developed and maintained by Finn Årup Nielsen.

Contents

[edit] Database struture

There are several structures in the Brede Database for organizing the data. The main structure is describing neuroimaging articles and have one or more "experiments" that is turns have one or more "location", i.e., structures for Talairach coordinates and their associated statistical information. Two other structures are for brain regions and "external components" i.e., topics such as cognitive component.

[edit] Experiment

The experiment structure ('Exp') is modeled after the associated structure in the early version of BrainMap.

woexp 
Brede Database identifier for each experiment
type 
Should always be 'exp' for this type of structure
capsuleDescription 
Short description/title of the experiment
freeFormDescription 
Longer description
labOfExperiment 
Organization that performed the experiment
specificTask 
Task in the experiment, modeled after BrainMap, see also CogPO
numberOfSubject 
Number of subjects in the experiment
behavioralDomain 
Behavioral domain, modeled after BrainMap, see also CogPO.
brainTemplate 
Template/stereotaxic space, e.g., CBA, HBA, MNI, SPM95, Talairach
scanner 
Brain scanner
tracer 
If positron emission tomography study, then the radiotracer.
woext 
Identifier for Brede Database 'external component', i.e., topic of the experiment. There might be multiple 'woext's. See also http://neuro.imm.dtu.dk/services/brededatabase/index_ext_alphabetic.html
woextNegative 
Identifier for Brede Database 'external component', e.g., if the experimental contrast was rest minus activation.

[edit] Brain regions

The taxonomy/ontology of brain regions is recorded in an XML file called worois.xml [1]. In this file each brain region is recorded in a Roi XML node with the following fields (XML tags). See also Brede Database/WOROI.

woroi 
Brede Database integer identifier for the brain region
name 
Canonical name for the brain region
abbreviation 
Zero or multiple abbreviations for the brain region
cocomacSite 
Zero or multiple string identifiers for corresponding regions in the CoCoMac database.
icbmLabel 
Identifier for the ICBM labeled brain. This atlas may not be available (or have changed?)
brainInfo 
Optional integer identifier for the BrainInfo/NeuroNames Web service for the corresponding brain regino
description 
Optional text description of the brain region
ibvdName 
Optional corresponding region in the Internet Brain Volume Database.
hammers 
Optional identifier for the atlas of Alexander Hammers. This atlas may not be public available.
meshUid 
Optional string identifier for the corresponding term in the MeSH
svarer 
Identifier for the atlas of Claus Svarer.
type 
A field always set to roi.
tzourioMazoyer 
Optional identifier for the Automatic Anatomical Labeling (AAL) atlas.
variation 
Zero or multiple abbreviations for the brain region
wikipedia 
Optional title of article in Wikipedia corresponding to the brain region
parent 
Zero or more identifiers for taxonomic broader brain regions, usually indicating part of relation.
child 
Zero or more identifiers for taxonomic narrower brain regions, usually indicating has part relation.

For brain regions in the Brede Wiki that is also in the Brede Database see the category Brain regions in Brede Database. For brain regions missing the Brede Database see the category Brain regions missing in Brede Database.


[edit] Topics

See Brede Database/WOEXT.

[edit] Researchers

Seee Brede Database/WOPER.

[edit] Papers

  1. Brede tools and federating online neuroinformatics databases
  2. The Brede database: a small database for functional neuroimaging
  3. Visualizing data mining results with the Brede tools

[edit] Third-party mentions

  1. A hemodynamic correlate of lateralized visual short-term memories
  2. Activation in the MT-complex during visual perception of apparent motion and temporal succession
  3. Application of neuroanatomical ontologies for neuroimaging data annotation
  4. BrainKnowledge: a human brain function mapping knowledge-base system
  5. Divide and conquer: A defense of functional localizers
  6. Diverting attention suppresses human amygdala responses to faces
  7. Exploring biological network dynamics with ensembles of graph partitions
  8. Informatics in neuroscience
  9. Lost in localization--But found with foci?!
  10. Lost in localization: the need for a universal coordinate database
  11. Neuroinformatics tools for functional MRI: experimental design and data analysis
  12. Online workbenches for neural network connections

[edit] Papers in the Brede Database

See Brede Database/WOBIB

[edit] References

  1. Finn Årup Nielsen (2009). "Visualizing data mining results with the Brede tools". Frontiers in Neuroinformatics 3: 26. doi: 10.3389/neuro.11/026.2009.
  2. Finn Årup Nielsen (2003). "The Brede database: a small database for functional neuroimaging". NeuroImage 19(2): missing pages.
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