W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > February 2006

Re: [HCLSIG] homologs for yeast proteins?

From: Pat Hayes <phayes@ihmc.us>
Date: Wed, 1 Feb 2006 12:41:00 -0600
Message-Id: <p06230915c006ade2dfb3@[]>
To: Eric Miller <em@w3.org>
Cc: chris mungall <cjm@fruitfly.org>, Alf Eaton <lists@hubmed.org>, public-semweb-lifesci@w3.org

>On Jan 31, 2006, at 5:05 PM, chris mungall wrote:
>>On Jan 31, 2006, at 1:46 PM, Eric Miller wrote:
>>>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 
>>>>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.
>>surely screen scraping should be a last resort, such as when the 
>>underlying database has no APIs or download option
>>all the data underlying amigo is available in a number of hopefully 
>>more sensible ways. See http://www.godatabase.org/dev
>Good to know. Do you think people just "know" the fact that the 
>underlying amigo is available? The link is helpful at the bottom of 
>the page, but a *consistent* convention this community could adopt 
>to clearly associate the data corresponding to the HTML page would 
>be extremely valuable.
>More specifically, I'd suggest for this page, the following template be used
><link rel="meta" type="application/rdf+xml" title="Data for 
>and help define such a consistent linking mechanism.

Seems like RDF/A should be relevant here. It will be a draft 
recommendation very soon, time to get ahead of the game? See 


IHMC		(850)434 8903 or (650)494 3973   home
40 South Alcaniz St.	(850)202 4416   office
Pensacola			(850)202 4440   fax
FL 32502			(850)291 0667    cell
phayesAT-SIGNihmc.us       http://www.ihmc.us/users/phayes
Received on Wednesday, 1 February 2006 18:41:09 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:24 UTC