[Go] Gene Symbols as GO synonyms

[Jennifer Deegan (nee Clark)]

Hi Judy,

We did think about this, but I remember that the group who work on p53 
were very keen that a term covering an activity of this gene product 
should carry a synonym 'p53' to help them find the term. I am reluctant 
to remove all gene symbols as synonyms because of that, but thought I 
would just tidy up these two problematic terms. We could certainly 
consider removing all gene symbol synonyms in the long term, but it 
seems to me that the effort required to track them all down and discuss 
individually whether they are required might not be worthwhile, since we 
have other time-consuming projects that are a higher priority. Would you 
agree?

Thanks for thinking about it.

Jen


Judith Blake wrote:

> 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
>>
>>
>>
> 

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium