[Go] Gene Symbols as GO synonyms

[Judith Blake]

Hi Jen,

When I search GO terms for 'p53', this does not come back as a synonym, 
although synonyms with the string 'p53' as part of the long series of 
strings as a synonym do come back.  So I don't think that argument holds 
anymore.  I agree that grinding through looking for synonyms that are 
gene symbols is not a productive use of time, but such synonyms, I 
think, should be removed as a matter of course while working on the 
ontology in general as they are found.  I do not see, if 'p53' is not an 
issue, where anything else would be an issue.

Does anyone object to having gene symbols routinely removed as found as 
synonyms?  Certainly the ontology editors can bring such synonyms 
forward if they think there might be an issue. what do you think Jen?

Judy


Jennifer Deegan (nee Clark) wrote:
> 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
>>>
>>>
>>>
>>
>