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The Brede Wiki: A social neuroinformatics web-service with structured information from neuroscience

FÅ Nielsen
2009 NeuroImage  
In the Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text.  ...  Conclusion A wiki promises a solution for the problem of data entry and data sharing in neuroscience. The templates of MediaWiki offer a flexible way to represent structured information.  ... 
doi:10.1016/s1053-8119(09)71701-x fatcat:nluinr3mqragbedf36qmmn72ea

Brede Tools and Federating Online Neuroinformatics Databases

Finn Årup Nielsen
2013 Neuroinformatics  
As open science neuroinformatics databases the Brede Database and Brede Wiki seek to make distribution and federation of their content as easy and transparent as possible.  ...  This paper describes the possible interconnections on different levels between the Brede tools and other databases. * The final publication is available at http://dx.  ...  Organizations get connected in a hierarchical structure in the Brede Wiki and may link to Wikipedia and Microsoft Academic Research.  ... 
doi:10.1007/s12021-013-9183-4 pmid:23666785 fatcat:xjltp6ttqngafgtowmjff4g2ae

Visualizing data mining results with the Brede tools

Finn A. Nielsen
2009 Frontiers in Neuroinformatics  
A few neuroinformatics databases now exist that record results from neuroimaging studies in the form of brain coordinates in stereotaxic space.  ...  With Brede Toolbox and Database combined, we setup automated workfl ows for extraction of data, mass meta-analytic data mining and visualizations.  ...  The Brede Toolbox can also use GraphViz for layout of other types of data that can be described as a network, e.g., from structural equation modeling of regional neuroimaging data.  ... 
doi:10.3389/neuro.11.026.2009 pmid:19668704 pmcid:PMC2723048 fatcat:nvn7mdv2cnhztosdoy5exj6zjm

Lost in localization: A solution with neuroinformatics 2.0?

Finn Årup Nielsen
2009 NeuroImage  
Here I discuss further issues and propose another angle to the solution of a universal coordinate database with the use of wiki technology.  ...  The commentary by Derrfuss and Mar (2009) discusses some of the limitations of the present databases and calls for a universal coordinate database.  ...  For the Brede Wiki a simple Matlab script allows for formatting coordinate lists from the SPM program in the style suitable for inclusion in the Brede Wiki.  ... 
doi:10.1016/j.neuroimage.2009.05.073 pmid:19497377 fatcat:oje4ea4sgbgk5bmnvgrpb3zerm

Scientific Collaborations: principles of WikiBridge Design [article]

Eric Leclercq, Marinette Savonnet
2010 arXiv   pre-print
This paper details the design principles ofWikiBridge, a semantic wiki.  ...  Semantic wikis, wikis enhanced with Semantic Web technologies, are appropriate systems for community-authored knowledge models. They are particularly suitable for scientific collaboration.  ...  Brede Wiki [7] contains information from published peer-reviewed neuroscience articles.  ... 
arXiv:1012.1743v1 fatcat:4xfycjkh35gkhf6e5m6umr4cbi

Action and Language Mechanisms in the Brain: Data, Models and Neuroinformatics

Michael A. Arbib, James J. Bonaiuto, Ina Bornkessel-Schlesewsky, David Kemmerer, Brian MacWhinney, Finn Årup Nielsen, Erhan Oztop
2013 Neuroinformatics  
We assess the challenges of studying action and language mechanisms in the brain, both singly and in relation to each other to provide a novel perspective on neuroinformatics, integrating the development  ...  of databases for encoding -separately or together -neurocomputational models and empirical data that serve systems and cognitive neuroscience.  ...  The Brede Wiki in turn links back to BODB's "Summary of Experimental Data" and "Literature" (and Brede Database) through hard-coded deep links.  ... 
doi:10.1007/s12021-013-9210-5 pmid:24234916 pmcid:PMC4101894 fatcat:j5ddog5unbf6tlbgn6mt4oj334

Action, Language and Neuroinformatics: An Introduction

Michael A. Arbib
2013 Neuroinformatics  
computational models for neuroscience, for providing databases for the very different forms of empirical data now exploited by neuroscience, and for linkage of data and models in systems and cognitive  ...  Database BODB is organized around two main ideas: (i) A brain model should be characterized not only by a structural ontology (the brain regions or finer structures to which it corresponds) but also by  ...  Brain Project of the University of Southern California, and organized by Michael A.  ... 
doi:10.1007/s12021-013-9212-3 pmid:24174261 fatcat:atfgtsw3bzhmrmftzz3yexksie

Knowledge Engineering for Historians on the Example of the Catalogus Professorum Lipsiensis [chapter]

Thomas Riechert, Ulf Morgenstern, Sören Auer, Sebastian Tramp, Michael Martin
2010 Lecture Notes in Computer Science  
In order to enable historians to collect, structure and publish prosopographical knowledge an ontology was developed and knowledge engineering facilities based on the semantic data wiki OntoWiki were implemented  ...  For access and exploration by other historians a number of access interfaces were developed, such as a visual SPARQL query builder, a relationship finder and a Linked Data interface.  ...  Acknowledgments We would like to thank our colleague Christian Augustin and all of the young researchers, involved in archival work and interviews, for their helpful comments and  ... 
doi:10.1007/978-3-642-17749-1_15 fatcat:i7m3h74lgzdubapjn3ojgnybni

Wikipedia Research and Tools: Review and Comments

Finn Årup Nielsen
2012 Social Science Research Network  
I here give an overview of Wikipedia and wiki research and tools. Well over 1,000 reports have been published in the field and there exist dedicated scientific meetings for Wikipedia research.  ...  It is not possible to give a complete review of all material published. This overview serves to describe some key areas of research. i  ...  A specific idea of Brede Wiki was also to maintain structured information in a machine readable format for data mining. 390, 391, 449 Related wikis summarizing academic work are Acawiki, WikiPapers  ... 
doi:10.2139/ssrn.2129874 fatcat:h4znerp2efhn5j5bdi5rl7addi

Lost in localization — But found with foci?!

David C. Van Essen
2009 NeuroImage  
content in a realistic time frame.  ...  Lost in localization: a solution with neuroinformatics 2.0? Neuroimage.], Hamilton [Hamilton, A., 2009. Lost in localization: a minimal middle way.  ...  Acknowledgments I thank Erin Reid for yeoman's work in data entry and curation, John Harwell and Ping Gu for excellent software design and development, Jessica Cohen, Jeff Phillips, Shawn Christ, and Donna  ... 
doi:10.1016/j.neuroimage.2009.05.050 pmid:19481158 pmcid:PMC2756522 fatcat:g3rdp53nnbavxnsxgr6fq4yam4

Using text mining to link journal articles to neuroanatomical databases

Leon French, Paul Pavlidis
2012 Journal of Comparative Neurology  
The electronic linking of neuroscience information, including data embedded in the primary literature, would permit powerful queries and analyses driven by structured databases.  ...  We find that many terms in the formal terminologies never appear in a JCN abstract, while conversely, many terms authors use are not reflected in the terminologies.  ...  In particular we thank Maryanne Martone, Stephen Larson and Anita Bandrowski for facilitating our additions to  ... 
doi:10.1002/cne.23012 pmid:22120205 pmcid:PMC3812935 fatcat:uc3qtuzh5raovgjtqpuhgwzlqy

Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application

Leon French, Po Liu, Olivia Marais, Tianna Koreman, Lucia Tseng, Artemis Lai, Paul Pavlidis
2015 Frontiers in Neuroinformatics  
Finally, we present a new web application that allows fast interactive browsing of the over 70,000 sentences indexed by the system, as a tool for accessing the data and assisting in further curation.  ...  Software and data are freely available at  ...  How much connectivity data is available in neuroscience abstracts? 4. Which species are used for connectivity studies?  ... 
doi:10.3389/fninf.2015.00013 pmid:26052282 pmcid:PMC4439553 fatcat:rgwdlnc4yfhdjjf4cdrf5p55jy

Can cognitive processes be inferred from neuroimaging data?

2006 Trends in Cognitive Sciences  
Using a Bayesian analysis of the BrainMap neuroimaging database, I characterize the amount of additional evidence in favor of the engagement of a cognitive process that can be offered by a reverse inference  ...  One particular practice that has become common is 'reverse inference', by which the engagement of a particular cognitive process is inferred from the activation of a particular brain region.  ...  Thanks to Angie Laird of the UT Health Science Center in San Antonio for performing the searches needed to produce Table 1 .  ... 
doi:10.1016/j.tics.2005.12.004 pmid:16406760 fatcat:yv4iwe6y2zdezhtka4ic4khmpa

Construction And Analysis Of The Time-Evolving Pain-Related Brain Network Using Literature Mining

Jihong Oh, Hyojin Bae, Chang-Eop Kim
2019 Journal of Pain Research  
We aimed to quantitatively investigate how the neuroscience field developed over time in terms of its concept on how pain is represented in the brain and compare the research trends of pain with those  ...  We defined 22 pain-related brain regions that appeared more than 100 times in the retrieved abstracts.  ...  Acknowledgments Disclosure The authors have declared that no competing interests exist in this work.  ... 
doi:10.2147/jpr.s217036 pmid:31802931 pmcid:PMC6801488 fatcat:rk3o2bfwwrgapfpkbxvg6lv35i

Application of neuroanatomical ontologies for neuroimaging data annotation

2010 Frontiers in Neuroinformatics  
In summary, we have produced a neuroanatomical ontology that harmonizes several different terminologies of neuroanatomical structures and cortical parcellation schemes.  ...  The annotation of functional neuroimaging results for data sharing and re-use is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation  ...  the Brede database (Nielsen et al., 2004) ; of these, SumsDB at least allows queries to be performed across parcellation schemes in a single database.  ... 
doi:10.3389/fninf.2010.00010 pmid:20725521 pmcid:PMC2912099 fatcat:oodol6ftmndl5g5folq6uknbmi
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