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 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 > >>>>>>> >>>>>>> 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@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@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@geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/go > > > > _______________________________________________ > Go mailing list > Go@geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > >