[Go] Gene Symbols as GO synonyms

Tue Apr 8 08:34:44 PDT 2008

this would work for me

judy

Jane Lomax wrote:
> Hi Judy - I'd be fine adding '-activity' to the gene symbol synonyms 
> if people think it would help - for mapping purposes I don't think it 
> would make any difference.
>
> Alex - these are prokaryotic mappings, and most of the genes are 
> prok-specific and therefore have no manual annotation (or often any 
> annotation) so not sure using ga files would work.
>
> Jane
>
>
> On Fri, 4 Apr 2008, Judith Blake wrote:
>
>> Jane,
>>
>> I am fine with Jen's comment that it's not a priority to spend extensive
>> time removing gene names as synonyms, and that some inclusion of
>> geneproduct-like synoyms is useful for seaching...for example, when we
>> were in the attitude of removing all functions that sounded like product
>> names, the product names were in fact what the community used as an
>> alias for the activity name.  WE have stopped that for the most part.
>> But I think the point here is that gene names should not, I think we are
>> agreeing, be 'nakedly' posted as synonyms, but rather could be posted
>> as, say,  "Bmp4-activity' .
>>
>> Jane, could you give an example where the gene symbol, nakedly, you
>> think should be included as a synonym?  or are you just pulling these
>> over....maybe for the enzymes, like before, we could add 'activity'?  or
>> is that too simiplistic or are you doing this bulk ?
>>
>> judy
>>
>>
>> Valerie Wood wrote:
>>> I'm still not sure why we have include them at all.
>>>
>>> In the long term it will confuse users because it might stop tem 
>>> being able to make the distinction between the ontology and the 
>>> annotations. Also, it is inconsistent, why do this for a few gene 
>>> names but not all, and also for some terms which a gene product 
>>> would be annotated to but not all, this can also lead to confusion, 
>>> because users might think that a gene name search will always work.
>>>
>>> Jen, was the p53 case correct? (as Judy pointed out there are no p53 
>>> synonyms), but 'p53 class' is included in the term name of some 
>>> terms, which is differrent.
>>>
>>> Val
>>>
>>>
>>> Chris Mungall <cjm at fruitfly.org> wrote:
>>>
>>>> On Apr 3, 2008, at 6:07 AM, 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?
>>>>>
>>>> This seems slightly awkward - we'd have to coordinate this with every
>>>> GO browser out there. And what about the RELATED synonyms that are
>>>> not gene products?
>>>>
>>>> How about introducing a new synonym category (called "gene" for
>>>> example)? Note that these synonyms would still be RELATED, there
>>>> would just be additional metadata indicating the context for the
>>>> synonym.
>>>>
>>>> I still don't think this is perfect. We shouldn't go overloading
>>>> existing tags just because it happens to help with searching in a few
>>>> cases.
>>>>
>>>>
>>>>> 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
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>
>>
>> _______________________________________________
>> 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