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BIRN Use Cases - and the BIRNLex controlled, lexical framework

William Bug William.Bug at drexelmed.edu
Sun Jun 25 12:30:20 PDT 2006


Dear GO Friends,

The BIRN Ontology Task Force has been working over the last few weeks  
to move 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] and invite  
you all to visit.

Some of the Use Cases assembled across BIRN - across the 3 test  
beds** - FBIRN, MBIRN, and mBIRN 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].  We are working to integrate others  
into the infrastructure, such as GENSAT [8], the Allen Brain Atlas  
[9], 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].  From the point-of-view  
of human access to these neuroimage data sets, at least on MBIRN, the  
very mature 3D Slicer anatomical analysis & visualization environment  
([19]) can provide a means by which researchers can make productive  
use of these images.

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

Within mBIRN, we've also been working on the specification and  
demonstration of a 3D Atlas Interoperability API ([20]) - one can be  
used both to power spatially-based, neuroscience data mediation  
services and to support interoperability between the > 35 3D  
anatomical visualization/analysis tools currently in use across the  
field (e.g., search on 'visualization' AND 'volume' at the Internet  
Analysis Tool Registry [21] - 53 items come up, but about 40 of them  
fall into the category of 3D anatomical visualization/analysis tools).

We recognize there will be a need for feedback.  More to the point -  
we welcome & encourage feedback as we proceed with the very complex  
and long-range task of providing a solid semantic foundation for the  
organization and searching of all the data being hosted within the  
BIRN infrastructure.  We expect to have a mailing list in place soon,  
and I will post information on how to use it to this group, when it  
is available.  In the meantime, I'd suggest you directly address  
feedback either to Maryann Martone (maryann at ncmir.ucsd.edu) co-chair  
of the BIRN-OTF or to me.

Cheers,
Bill

** The three BIRN testbeds:
	-  Functional Imaging Research of Schizophrenia (aka, Function BIRN  
or FBIRN):
		Primarily consisting of functional MRI studies correlated to human  
cognitive & behavioral assessments used in the examination of various  
aspects of schizophrenia [2];
	- Brain Morphometry BIRN (aka Morphometry BIRN or MBIRN):
		These groups focus on correlating Morphological MRI, as well as DTI  
for examining connectivity and axonal profiles,  with various  
clinical measures of neurodegenerative disease such as depression,  
Alzheimer's, and other forms of mild cognitive impairment [3];
	- Multi-scale Mouse Models of Neurodegerative Dieases (aka Mouse  
BIRN or mBIRN)
		This BIRN testbed brings together researchers working on gene  
expression, 3D brain atlasing, and various forms of light & electron  
microscopy studying cells and brain regions in with a focus on mouse  
models of neurodegenerative disease [4].


[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
[19] http://www.slicer.org/
[20] http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/ 
AtlasStateExchange
[21] http://www.cma.mgh.harvard.edu/iatr




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 at DrexelMed.edu







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