Thank you! Your answer confirms what I expected. There should be no "gray" items in OMIM Phenotype Loci track.
But what about the "OMIM Genes" track? Should there still be "gray" items in that track? I have been told by someone that those items are "low quality" annotations, and that is why you include the possibility to turn them off. Can you give any recommendations about whether those items should or should not be displayed ? Ed -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Friday, July 06, 2012 4:31 PM To: Erwin, Ed Cc: [email protected] Subject: Re: [Genome] OMIM Phenotypes with map key "null" Hi Ed, The fact that you can see any items with phenotype key 0 in the OMIM Pheno Loci track is a bug . . . those items are not supposed to be included in the track at all. So, your #2 is true: > 2) It should never be possible to see items with phenotype key 0, and > thus "Reset" should turn off the ability to see items where key is > not 1,2,3 or 4. We have logged the bug in our tracking system, but I don't have a time frame yet for when it might be fixed. Thank you for reporting the problem, and sorry for the confusion it has caused! If you see any other problems or have any further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 7/6/12 3:03 PM, Erwin, Ed wrote: > Thank you for reminding me about the "Reset" feature. > > But I think there is some mistake in the default configuration of the > "OMIM Pheno Loci" track. > > Using "Click here to reset..." resets the configuration to a state > where the "OMIM Pheno Loci" track displays items with phenotype key > 0, 1, 2, 3, 4. > > But, after that, if you visit the configuration page for "OMIM Pheno > Loci", even if you *make* *no* *changes* to the default settings, the > items with phenotype key 0 will disappear, and only the ones with key > 1, 2, 3, 4 remain. After that, there is no way to turn back on the > ones with key 0. > > Track configuration page: > http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr3&g=omimLocation > > The "Click here to reset..." feature, is thus putting this track into > a state that it is impossible to get into through normal operation of > the browser. > > There are two possibilities, and I need to know which is correct: 1) > It should be possible to see items with phenotype key 0 if the user > wants to, and thus that option should be included on the track > configuration page, or 2) It should never be possible to see items > with phenotype key 0, and thus "Reset" should turn off the ability to > see items where key is not 1,2,3 or 4. > > Ed > > > -----Original Message----- From: Luvina Guruvadoo > [mailto:[email protected]] Sent: Monday, July 02, 2012 10:00 AM To: > Erwin, Ed Cc: [email protected] Subject: Re: [Genome] OMIM > Phenotypes with map key "null" > > Hi Ed, > > Your colleague should be able to re-set her options by resetting her > cart. To do this, click on "Click here to reset..." from the Genome > Browser Gateway page > (http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg19). > > Please contact us again at [email protected] if you have any > further questions. > > --- Luvina Guruvadoo UCSC Genome Bioinformatics Group > > > On 6/28/2012 2:32 PM, Erwin, Ed wrote: >> I am seeing some strange behavior with the track "OMIM Phenotypes - >> Gene Unknown" >> >> According to the track settings page for this track, it is supposed >> to only show annotations where the "phenotype map key" is 1, 2, 3, >> or 4. And the user has the ability to turn on/off each of those >> individual values from the configuration page: >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr3&g=omimLocation >> >> When I visit the browser, it is true that I only see values where >> it is 1, 2, 3 or 4. >> >> But when my colleague, on a different computer, visits the same >> location, she sees some additional items which do not have the key >> 1,2, 3 or 4. These additional items are drawn in gray, and >> correspond to OMIM phenotype map key "null" or "0". >> >> Is it possible that in some past version of the browser, the >> configuration page allowed her to choose to display "0" and the >> browser has persisted that choice? If so, how can she re-set her >> options? >> >> Thanks, Ed Erwin >> >> >> >> _______________________________________________ Genome maillist - >> [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
