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Re: [BioRDF] Telcon

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Fri, 24 Feb 2006 11:40:27 -0500
Message-Id: <BC9EA984-4F64-4379-99C6-8F3A3D015042@gmail.com>
To: public-semweb-lifesci <public-semweb-lifesci@w3.org>


On Feb 24, 2006, at 8:41 AM, Susie Stephens wrote:

> Here's the conference call information for Monday.
>
> Lets also decide who is going to be working on which NCBI data  
> sources.

Do we have list of those resources that we will be working from?

We need to discuss which are important for us, some idea of use case.

There is *a lot* of information at NCBI. I think we need to targeted  
some specific, limited size, sets that
would be relevant to the domain so that we don't get bogged down on  
scaling issues.

Some ideas:

Neuroactive substances from pubchem. We would need someone to propose  
a list or a query that retrieves a reasonable list. Need to define a  
subset of interesting information from the entry.

Gene expression tissue localization information, so we can do a query  
to find those expressed in neural tissues.

Omim records for neurological diseases - text and links to papers.  
Need do get list or query. Issue: Much useful information is freetext.

Geo array to tissue map. Problem: This tends to be freetext in the  
source or description fields.

Also, we should review some of the resources in the list that  
Matthias sent: http://big.sfn.org/NDG/site/eavObList.asp? 
c=81&menu_item=dblist

Some candidates found in quick browsing there:

Alzforum has a resource for antibodies http://www.alzforum.org/res/ 
com/ant/default.asp

SynDB: Database of Synaptic Proteins http://syndb.cbi.pku.edu.cn/  
information on proteins known or predicted to be related to the  
synapse or synaptic activity

Functional MRI Data Center, Dataset metadata such as http:// 
www.fmridc.org/f/fmridc/protege/view_experiment.html?expid=2%2d2005% 
2d119CE&id=csXtuKzc. Problem: Freetext.

Mapping of abnormality type to images in the Whole Brain Atlas,  
http://www.med.harvard.edu/AANLIB/home.html. Not controlled  
vocabulary - needs some structuring/ontology work.

Perhaps Tim Clark could suggest some resources that are on his  
groups' target list, and the rest of us spend some time scouting  
around the links looking for promising sources.

Regards,
Alan
Received on Friday, 24 February 2006 16:40:33 GMT

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