BIRN Use Cases - and the BIRNLex controlled, lexical framework

Hi Eric,

I've been working with other BIRN Ontology TF members on and off over  
the last few weeks to start moving some of our "private" Wiki work to  
the public BIRN Wiki pages.

We now have a public Wiki page for the BIRN OTF here [1]

Some of the Use Cases assembled across BIRN - across the 3 test beds  
- FBIRN (functional MRI used in human cognitive & behavioral  
assessments associated with schizophrenia [2]), MBIRN (Brain  
Morphometry BIRN - standard MRI and DTI for examining connectivity  
and axonal profiles - correlated with various clinical measures of  
neurodegenerative disease such as depression, Alzheimer's, and other  
forms of mild cognitive impairment [3]), and mBIRN (Multi-scale Mouse  
Models of Neurodegerative Dieases - bringing together researchers  
working on gene expression, 3D brain atlasing, and various forms of  
light & electron microscopy studying cells and brain regions in mouse  
models of neurodegenerative disease [4]) are already available on  
this page with more to come.

mBIRN includes several very large neuroinformatics data repositories  
- e.g., the Cell-Centered Database (CCDB [5]), GeneNetwork/WebQTL  
[6], the Mouse Brain Library [7] and working to integrate others into  
the infrastructure, such as GENSAT [8], the Allen Brain Atlas [9],  
and the neuro- elements from the Mouse Atlas of Gene Expression from  
Vancouver, BC [10], etc..

MBIRN & FBIRN labs (BIRN has ~ 70 participating labs across the  
country ([11] & [12])) are also accruing large neuroimage  
repositories.  These will ultimately all be accessible publicly from  
the BIRN SRB infrastructure ([13] & [14]) with associated metadata as  
instances of the BIRN XCEDE XML Schema [15].

Connections to other human/primate repositories outside of BIRN -  
e.g., the fMRI Data Center [16] and the literature informatics  
projects BrainMap [17] and CoCoMac [18] are being actively pursued.

Cheers,
Bill

[1] http://xwiki.nbirn.net:8080/xwiki/bin/view/+BIRN-OTF-Public/Home
[2] http://www.nbirn.net/TestBeds/Function/index.htm
[3] http://www.nbirn.net/TestBeds/Morphometry/index.htm
[4] http://www.nbirn.net/TestBeds/Mouse/index.htm
[5] http://ccdb.ucsd.edu/index.htm
[6] http://www.genenetwork.org/
[7] http://www.mbl.org/
[8] http://www.ncbi.nlm.nih.gov/projects/gensat/
[9] http://www.brain-map.org/ 
welcome.do;jsessionid=E0A2DE018D51F6A8320FE3822EB6ADD6
[10] http://www.mouseatlas.org/
[11] http://www.nbirn.net/TestBeds/Function/Organization.htm
[12] http://www.nbirn.net/TestBeds/Morphometry/Organization.htm
[13] http://www.nbirn.net/Resources/Users/Applications/SRB/index.htm
[14] http://www.npaci.edu/DICE/SRB/
[15] http://www.nbirn.net/Resources/Downloads/BXH_Tools/index.htm
[16] http://www.fmridc.org/f/fmridc
[17] http://www.brainmap.org
[18] www.cocomac.org



Bill Bug
Senior Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu


This email and any accompanying attachments are confidential. 
This information is intended solely for the use of the individual 
to whom it is addressed. Any review, disclosure, copying, 
distribution, or use of this email communication by others is strictly 
prohibited. If you are not the intended recipient please notify us 
immediately by returning this message to the sender and delete 
all copies. Thank you for your cooperation.