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Re: Another brain connectivity map

From: William Bug <William.Bug@DrexelMed.edu>
Date: Mon, 12 Mar 2007 14:00:11 -0700
Message-Id: <14AA1894-8CA1-40AA-A70E-FCBBCBEF6827@DrexelMed.edu>
Cc: John Barkley <jbarkley@nist.gov>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Sorry - I've been swamped with this all week BIRN meeting.  I'm in a  
programmer's meeting now.

Yes - this is the UC Davis Human Brain Project group.  They have a  
lot of very useful multiple species brain atlases.  The problem will  
be with the actually terminology they use.  It doesn't match  
NeuroNames, nor does it match BAMS.  Some of the issues related to  
cross-species mapping of brain regions - a real tough scientific  
problem several groups are actively working on - some within BIRN.   
The other issue is they simply have their own terms that ARE in fact  
semantically equivalent to regions defined in NeuroNames.  I might be  
able to do a fairly quick mapping to the neuroanatomy we have in  
BIRNLex which does link to NN and to SOME of BAMS.

I've also been working with someone in Maryann's lab re: BAMS  
connection from our OWL ontologies.  I hope to get to that more  
concretely after this meeting is over Wednesday morning.

Regarding gene-indexed images in general, we should probably look at  
the UCSC VisiGene browser (related to the UCSC Genome Browser):
	http://genome.ucsc.edu/cgi-bin/hgVisiGene

For the most part, this consists of a gene-name index aggregation of  
in situ statined images from GENSAT and MGI/Jackson Labs.  Alan has  
already worked on a link to GENSAT which is likely much more  
semantically rich (indexes ALL the GENSAT meta data - not just gene  
name) than this repository.  MGI images are valuable to link to, as  
there are many times when a particular scientific or clinical  
question may lead you to ask "Where else in the body is this gene  
expressed?"

Cheers,
Bill


On Mar 12, 2007, at 1:32 PM, Alan Ruttenberg wrote:

>
> Might be good to take a look at this with a mind towards  
> representing BAMS in a way that both the resources could be used  
> together.
> -Alan
>
> http://brainmaps.org/abbrevslist.php?export=xml
>

Bill Bug
Senior Research 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
Received on Monday, 12 March 2007 21:00:30 UTC

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