[Go] Gene Symbols as GO synonyms

[Jim Hu]

I agree with Judy that removing them from all terms is a good idea.   
If us microbiologists ever get our act together and start getting all  
the genes from metagenomics, you'll be glad you did! ;)

Jim


On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:

> I agree with your proposal.
>
> Would you not remove gene symbols as synonyms from all terms?
>
> Judy
>
> Jennifer Deegan (nee Clark) wrote:
>> Hi,
>>
>> A couple of GO terms currently contain a problematically large  
>> number of
>>  gene symbols
>> as related synonyms.
>> The synonyms were imported into the OBO file during updates from  
>> Enzyme
>> Commission data.
>>
>> The synonyms are a problem because they mess up the display in GO
>> browsers. For example:
>>
>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654
>>
>> They are also confusing for users as they resemble annotations, but  
>> are
>> only related synonyms.
>>
>> To resolve this problem, on 16th April we are going to remove the  
>> list
>> of gene products as related synonyms from the following terms:
>>
>> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
>> (201 gene symbols included as synonyms)
>>
>> GO:0004715 (non-membrane spanning protein tyrosine kinase activity)  
>> (84
>> gene symbols included as synonyms)
>>
>> If you have any objection to this removal please reply to Jennifer
>> Deegan and Emily Dimmer.
>>
>> Thanks,
>>
>> Jennifer and Emily.
>>
>>
>>
>
>
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=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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