[Go] Gene Symbols as GO synonyms

[Michael Ashburner]

That sounds a good medium solution Jane.

Michael

On 3 Apr 2008, at 06:07, Jane Lomax wrote:

> Hi Judy - the gene symbol synonyms can sometimes be very useful for  
> the
> purposes of mappings, especially for things like enzymes where some  
> groups
> use the gene symbol in their vocabulary term name (this has been  
> the case
> for the IMG and FIGS mappings recently). So I'd rather not see them
> removed completely.
>
> However I do agree that seeing them can be very confusing for users  
> - I
> wonder whether we could agree to suppress RELATED synonyms in the  
> GO interfaces?
> Maybe only show them when they match a search?
>
> jane
>
>   On Thu, 3 Apr 2008, 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
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go