[Go] Gene Symbols as GO synonyms

[Jennifer Deegan (nee Clark)]

Hi Judy,

It sounds fine to me, but I'd be interested to wait for a little while 
and hear if there are others who feel that these synonyms are useful.

Thanks,

Jen



Judith Blake wrote:

> 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.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>
>>>>
>>>> =====================================
>>>>
>>>> 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