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Re: [HCLSIG] homologs for yeast proteins?

From: chris mungall <cjm@fruitfly.org>
Date: Tue, 31 Jan 2006 13:41:20 -0800
Message-Id: <7eed1623794dc0a9dea5e1afc3accd12@fruitfly.org>
Cc: jluciano@predmed.com, jluciano@gmail.com, public-semweb-lifesci@w3.org
To: Eric Jain <Eric.Jain@isb-sib.ch>

On Jan 31, 2006, at 12:36 PM, 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.

I disagree - annotation using particular terms are exactly the kind of  
thing you need semantic web magic for. In this particular case 31930  
has no is_a or part_of children, so extra magic would buy you nothing;  
but for other queries you absolutely need to do inference to get other  
implied terms; and this inference will have to be more sophisticated as  
more relations from the OBO relations ontology are used in other OBO  
ontologies, and as more annotations are made by composing anonymous  
classes from a mixture of OBO ontologies.

>
> 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...

or the data sources; the GO database is the definitive source for gene  
products annotated using GO:

http://www.godatabase.org/cgi-bin/amigo/go.cgi? 
view=details&show_associations=list&search_constraint=terms&depth=0&quer 
y=GO:0031930&session_id=9683b1138739427

yields 6 yeast genes:

  LST8    S000004951
  MKS1    S000005020
  RTG1    S000005428
  RTG2    S000003221
  RTG3    S000000199
  TOR1    S000003827

You can then follow the links to the gene descriptions on SGD and fetch  
homologs from there;

Or you can go to
http://inparanoid.cgb.ki.se/index.html

and paste in the IDs one at a time, get the ensembl IDs for the human  
orthologs, and resolve these to a more standard ID system, being aware  
of the semantics of each ID to ID transitiion (eg proteins to genes)  
and the implications

Looks like we have our work cut out for us...
Received on Wednesday, 1 February 2006 22:56:15 GMT

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