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Re: [HCLSIG] homologs for yeast proteins?

From: Eric Miller <em@w3.org>
Date: Tue, 31 Jan 2006 16:46:59 -0500
Message-Id: <337AAF70-C4DD-4805-AFFA-A514B7DE69D9@w3.org>
Cc: public-semweb-lifesci@w3.org
To: Alf Eaton <lists@hubmed.org>

On Jan 31, 2006, at 3:56 PM, Alf Eaton wrote:

> Eric Jain wrote:
>> Joanne Luciano wrote:
>>> An MD I met with last week mentioned briefly the desire to obtain  
>>> homologs
>>> for yeast proteins with the GO ID 0031930.  With it was a request  
>>> for other
>>> suggestions for querying proteins with this ontology assignment  
>>> (looking for
>>> mammalian homologs).
>>> Can the semantic web help with this or is it already basic and  
>>> solved, in
>>> which case, can someone point me or fill in the details?  Where  
>>> should I go?
>>> What questions should I  ask?
>> Semantic web technologies can help make certain things simpler to  
>> implement -- and therefore allow things to be implemented that  
>> would not have been feasible otherwise. But tasks such as listing  
>> all proteins for an organism that have been tagged with a specific  
>> term are simple enough to be supported even without any semantic  
>> web magic, see http://pir.uniprot.org/, for example. This site  
>> also allows you to run similarity searches on the matching entries  
>> to find homologs.
>> Now in this particular case it looks like you are out of luck: No  
>> yeast proteins have been associated with GO:0031930. Often the  
>> main limiting factor are not the tools, but the available data...
> There are S. cerevisiae proteins assigned to GO:0031930 though, you  
> can see them here: <http://tinyurl.com/d2dm9>

I started writing a piggy bank [1] scraper using solvent [2] to make  
explicit the data thats implied in the HTML tables when I noticed the  
XML link [3] at the bottom of the page.

Turns out this "XML" link points to what looks like RDF/XML (but not  
quite). Anyone know who to contact to get this corrected? Bonus  
points if you're willing to own this action item and be the person to  
make the contact :)

[1] http://simile.mit.edu/piggy-bank/
[2] http://simile.mit.edu/solvent/
[3] http://www.godatabase.org/cgi-bin/amigo/go.cgi? 

eric miller                              http://www.w3.org/people/em/
semantic web activity lead               http://www.w3.org/2001/sw/
w3c world wide web consortium            http://www.w3.org/
Received on Tuesday, 31 January 2006 21:47:06 UTC

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