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Re: use cases

From: kc28 <kei.cheung@yale.edu>
Date: Wed, 22 Mar 2006 19:53:17 -0500
To: Tim Clark <twclark@nmr.mgh.harvard.edu>
Cc: public-semweb-lifesci@w3.org
Message-id: <4421F17D.9060906@yale.edu>

Hi Tim,

I agree with what you said. We should consider Alzforum (Alzheimer  
Disease) and come up with a use case that is practical to 
neuroscientists. I talked to Gordon Shepherd (who is a neuroscientist 
and the PI of SenseLab) about such a use case for our SenseLab task. He 
suggested the following use case.

Question: What experimental data is there on the earliest expression of  
tangles and plaques in relation to the different integative sites of a 
cortical pyramidal neuron? 

Answer:  Start in NeuronDB (which is a subdatabase of SenseLab) with a 
pyramidal cell in the neocortex or the hippocampus and ask what are the 
normal membrane properties in different soma-dendritic compartments; 
consult annotations and use pubmed links if desired.  Then link to 
BrainPharm (which is also a subdatabase of SenseLab) for experimental 
data from animal models on the early appearance of intracellular tangles 
and extracellular plaques related to those properties, for insights into 
how the pathology may be impacting normal membrane properties.  Consult 
annotations and use pubmed if desired.  Then link to Alzforum to the 
corresponding site(s) for data on genes and descriptions of plaques and 
tangles in animal models for correlation with behavioral effects. This 
will enhance the effort to identify the earliest effects of AD pathology 
on normal membrane properties of vulnerable neurons. BrainPharm will 
also identify pharmacological agents that may be effective in humans and 
different animal models at delaying or preventing the appearances of the 

Any thoughts?



Tim Clark wrote:

> Group
> I'd like to suggest a broadening of these use cases in two ways.
> (1) We have significant involvement (at least for now) from some  
> people with an outstanding community web resource on Alzheimer  
> Disease, the Alzforum (www.alzforum.org).  It seems a shame not to  
> talk a little more about Alzheimer disease.  I think June Kinoshita  
> might be willing to offer one or more very practical AD-related use  
> cases.
> There is also the Neurocommons project, with a strong focus on HD.   
> My group, as well, works on projects in HD, Parkinson's and AD.  How  
> dissimilar are these disorders in terms of the kinds of practical  
> problems of knowledge organization (and content requirements) faced  
> by researchers?  I maintain, they are not much different.
> (2) I suggest we think more about what information would be most  
> useful to scientists in determining what experiments to do, how to do  
> them, and how to interpret the results. More practical is better.
> Best
> Tim
Received on Thursday, 23 March 2006 00:58:58 UTC

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