<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div><br></div>I agree with Judy that gene symbols are not synonyms for GO terms. After all, the whole point of GO is that each gene should have three or more GO terms, and each GO term is associated with many genes across lots of organisms. That's just not what "synonym" means to me. <div><br></div><div><div>On the other hand, I understand and sympathize with Jen's explanation for why the group wanted p53 in the term record. Now that the associations are there, you can just look for the gene name in the gene associations, but while since the annotation process is not complete, there are other situations where finding terms is helped by having some gene names "associated" with a term at a level that would not be accepted as a completed annotation - i.e. no evidence code or reference. I think the gene names here are still potentially useful in that way; not as true synonyms, but as listings of examples to guide curation. I'm wondering if something like that would still be useful to have in the term record. </div><div><br></div><div>Not sure what to call it or how to implement, though. Example is too broad. I'm thinking that you don't just want examples, you want the cases where something is a paradigm for that GO term. For example, for GO:0030983:mismatched DNA binding, mutS would be a paradigm example, along with the MSH _family_ of proteins. But listing every MSH gene from every organism would be overkill. For broader things like ATPase activity, you wouldn't want to pick a particular example as a paradigm, as that molecular function is connected to too many disparate things.</div><div><br></div><div>I don't think RELATED captures this notion. I'd almost prefer to see just freetext comments, as I suspect that the kind of knowledge from fuzzy examples I'm talking about hre is not a good ontological idea.</div><div><br></div><div>Jim</div><div><br></div><div><br><div><html>On Apr 3, 2008, at 5:46 AM, Judith Blake wrote:</html><br class="Apple-interchange-newline"><blockquote type="cite">Hi Jen,<br><br>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.<br><br>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?<br><br>Judy<br><br><br>Jennifer Deegan (nee Clark) wrote:<br><blockquote type="cite">Hi Judy,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks for thinking about it.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Jen<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Judith Blake wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">not the least because they aren't synonyms....<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">judy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Jim Hu wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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! ;)<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Jim<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I agree with your proposal.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Would you not remove gene symbols as synonyms from all terms?<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Judy<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Jennifer Deegan (nee Clark) wrote:<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi,<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">A couple of GO terms currently contain a problematically large number of<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> gene symbols<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">as related synonyms.<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The synonyms were imported into the OBO file during updates from Enzyme<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Commission data.<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The synonyms are a problem because they mess up the display in GO<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">browsers. For example:<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654 <<a href="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</a>> <br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">They are also confusing for users as they resemble annotations, but are<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">only related synonyms.<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">To resolve this problem, on 16th April we are going to remove the list<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">of gene products as related synonyms from the following terms:<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">GO:0004714 (transmembrane receptor protein tyrosine kinase activity)<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">(201 gene symbols included as synonyms)<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">GO:0004715 (non-membrane spanning protein tyrosine kinase activity) (84<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">gene symbols included as synonyms)<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">If you have any objection to this removal please reply to Jennifer<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Deegan and Emily Dimmer.<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Jennifer and Emily.<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Go mailing list<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Go@geneontology.org <<a href="mailto:Go@geneontology.org">mailto:Go@geneontology.org</a>><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://fafner.stanford.edu/mailman/listinfo/go">http://fafner.stanford.edu/mailman/listinfo/go</a><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">=====================================<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Jim Hu<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Associate Professor<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dept. of Biochemistry and Biophysics<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">2128 TAMU<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Texas A&M Univ.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">College Station, TX 77843-2128<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">979-862-4054<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><br><br></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">=====================================</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Jim Hu</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Associate Professor</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Dept. of Biochemistry and Biophysics</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">2128 TAMU</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Texas A&M Univ.</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">College Station, TX 77843-2128</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">979-862-4054</font></p></div><br class="Apple-interchange-newline"></span> </div><br></div></div></body></html>