[Go] Gene Symbols as GO synonyms

[Judith Blake]

not the least because they aren't synonyms....

judy

Jim Hu wrote:
> 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 
>>> <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
>
>
>