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Re: [OBO-Edit Working Group] Cross Product editor: show name and IDin genus field [was Re: Cross Product editor: synonymconverted to term name]
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From: Alexander D. <ad...@in...> - 2011-12-08 15:05:38
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Hi Nomi, Thanks for these improvements. I think I like the style you presented in the screenshot better, with "synonym of." Will there be a new rc/beta version available to test relatively soon? Best regards, Alex On 12/8/11 7:06 AM, Walls, Ramona wrote: > > That looks great Nomi. Either way is fine with me. > > Ramona > > _____________________________ > Ramona Walls > Post-doctoral Researcher/Plant Ontology Curator > New York Botanical Garden > 2900th Southern Blvd. > Bronx, NY 10458 > (718)817-8173 > (516)885-8005 > > > > -----Original Message----- > From: Nomi Harris [mailto:nlh...@lb...] > Sent: Wed 12/7/2011 5:15 PM > To: Alexander Diehl > Cc: gen...@li... > Subject: Re: [OBO-Edit Working Group] Cross Product editor: show name > and IDin genus field [was Re: Cross Product editor: synonymconverted > to term name] > > I've made another improvement: the synonyms in the pulldown > autocomplete list now are marked as synonyms, and the term name of the > parent term is also shown. Unfortunately, this extra information is > often truncated because the pulldown menu isn't wide enough, but there > should be enough information there to at least alert you that it's a > synonym. > > > I also tried a style with "SYNONYM: " at the beginning, e.g., > "SYNONYM: maltose degradation (GO:0000025)". If you like that better, > or have other suggestions, please speak up (soon). > > Nomi > > On Dec 2, 2011, at 6:54 AM, Alexander Diehl wrote: > > > Hi Nomi, > > > > This looks great and should be a great help in selecting the correct > term in the XP tab. > > > > Thanks, > > > > Alex > > > > > > On 12/1/11 4:19 PM, Nomi Harris wrote: > >> > >> On Dec 1, 2011, at 2:00 AM, Dr Midori A. Harris wrote: > >> > >>> Hi, > >>> > >>> Going off on a tangent from Alex's suggestion, I would also love > it if we > >>> could put IDs in the Intersection Genus box -- that would avoid a > lot of > >>> the name/synonym confusion, and for some terms would mean a lot > less typing. > >> Good news--I was able to do this. It was not easy--the autocomplete > stuff is buried deep in the bowels of the BBOP library--but since I > had been poking around in there already in pursuit of the cross > product bug that turned out not to be a bug, I thought I might as well > work on this while I still remembered how it all worked. > >> > >> Now the genus field shows the ID in parentheses after the > term/synonym name. (Is that the format that you guys like? It's easy > to change if you tell me what you'd prefer.) > >> > >> > >> > >> After choosing one: > >> > >> > >> > >> After you commit and then go back to the Cross Products tab and > look at the genus, it's changed to the term name for the ID you > selected (but you'd have to remember the ID to realize that's why your > selection changed): > >> > >> > >> > >> Does this seem ok? > >> > >> Has anyone found any misbehavior in the cross product editor that's > not a silent synonym conversion (or the inability to delete a genus > once you've added one)? > >> > >> Nomi > >> > >>> > >>> > >>> Just a convenience, so not a high priority. > >>> > >>> Midori > >>> > >>> On Wed, 30 Nov 2011, Alexander Diehl wrote: > >>> > >>>> Nomi, > >>>> > >>>> One thing that might help would be to display the term ID of the > term in the > >>>> field itself either before or after the term name. This would > help to ensure > >>>> that the expected term is being picked from the correct ontology, > since some > >>>> term names are the same as synonyms for other terms in the same > or even other > >>>> ontologies. > >>>> > >>>> Thanks for all you help on figuring out this problem, > >>>> > >>>> Alex > >>>> > >>>> > >>>> On 11/30/11 1:09 PM, Nomi Harris wrote: > >>>>> I have done a bunch more testing on this, and have realized that > what > >>>>> seemed like a bug (selected genus getting replaced by a > different one) is > >>>>> in fact not really a bug, though it's behavior that you wouldn't > >>>>> necessarily expect. > >>>>> > >>>>> Here's the example I gave of the misbehavior: > >>>>>> It now looks like this, right before I click Commit: > >>>>>> > >>>>>> > >>>>>>> As soon as I commit, both the genus and the differentia change > to other > >>>>>>> terms (terms that weren't even in the pulldown lists!) > >>>>>>> > >>>>>>> > >>>>>>> What I discovered is that > >>>>>>> (1R,4R)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-one is in fact a > synonym of > >>>>>>> ( R )-camphor--it doesn't exist as an independent primary term > name. The > >>>>>>> autocomplete dropdown offers you synonyms as well as term > names, but if > >>>>>>> you choose a synonym, it silently converts that to the primary > term name, > >>>>>>> since there isn't a term with the name you selected. > >>>>>>> > >>>>>>> I don't know if that's desirable behavior, but it's not actually a > >>>>>>> bug--the changed genus is not just random. > >>>>>>> > >>>>>>> I was unable to find any other examples where the > cross-product editor > >>>>>>> changed the chosen genus to something other than the term name > for which > >>>>>>> a synonym had been selected. If there are other cases where it > >>>>>>> misbehaves, I need examples. > >>>>>>> > >>>>>>> I did manage to get it into a state at one point where I > couldn't remove > >>>>>>> the selected-for-me genus--if I tried to erase it or type > something > >>>>>>> different, it quickly put the old one back over whatever I > typed. That is > >>>>>>> a bug, but I haven't yet gotten it to happen repeatably. It is > possible > >>>>>>> that this bug accounts for some of the cases where the saved > genus is > >>>>>>> different from what you thought you typed, if it did that > reversion and > >>>>>>> you didn't notice before you clicked Commit. > >>>>>>> > >>>>>>> Please send me some repeatable examples of cross-product editor > >>>>>>> misbehavior! > >>>>>>> > >>>>>>> Nomi > >>>>>>> > >>>>>>> > >>>>>>> On Nov 17, 2011, at 2:42 PM, Nomi Harris wrote: > >>>>>>> > >>>>>>>> On Nov 16, 2011, at 7:46 PM, Alexander Diehl wrote: > >>>>>>>> > >>>>>>>>> 4) I also made a few cross products today -- for one the > wrong genus > >>>>>>>>> term got saved, for another no genus term got saved. > >>>>>>>> I did some more investigation on this. The bad news is that cross > >>>>>>>> products don't seem to get saved reliably. The good news is that: > >>>>>>>> 1. I can get this problem to happen repeatably (in current > and past > >>>>>>>> versions) > >>>>>>>> 2. The behavior was the same (or even worse) all the way back > to v2.00. > >>>>>>>> > >>>>>>>> I'm not sure how hard it would be to fix this bug. It was > reported as > >>>>>>>> far back as 2008: > >>>>>>>> > https://sourceforge.net/tracker/index.php?func=detail&aid=2126697&group_id=36855&atid=418257 > <https://sourceforge.net/tracker/index.php?func=detail&aid=2126697&group_id=36855&atid=418257> > >>>>>>>> "Sometimes it loses what I enter in the xp tab altogether, > sometimes it > >>>>>>>> keeps everything except the last differentia altogether." > >>>>>>>> and > >>>>>>>> > https://sourceforge.net/tracker/index.php?func=detail&aid=2008169&group_id=36855&atid=418257 > <https://sourceforge.net/tracker/index.php?func=detail&aid=2008169&group_id=36855&atid=418257> > >>>>>>>> "I can' t create any xps in any gui modality (more precise, I > can create > >>>>>>>> them, but they are lost as soon as I switch to anoter class, > even when > >>>>>>>> committing these class modifications or save the whole file: > I create a > >>>>>>>> xps, and then commit, change to another class, and when I go > back again > >>>>>>>> to the xps I created, all the newly specified genus and > differrentiae > >>>>>>>> are lost." > >>>>>>>> > >>>>>>>> Amina closed these bugs as Fixed on 2008-10-06, but I suspect > she didn't > >>>>>>>> try going to another term and then going back to the one > you'd edited to > >>>>>>>> see the problem (see below). > >>>>>>>> > >>>>>>>> > >>>>>>>> Here are some more detailed notes about how I observed the > bug, and its > >>>>>>>> behavior in different versions. > >>>>>>>> > >>>>>>>> First, to see the bug, you don't even have to use a fancy > ontology like > >>>>>>>> CL.obo--the camphor_catabolism sample ontology in > test_resources shows > >>>>>>>> it. > >>>>>>>> > >>>>>>>> 1. After loading camphor_catabolism.obo, select a genus from the > >>>>>>>> pulldown list (but not the first one on the list). (As an > aside, the > >>>>>>>> choices in this pulldown menu seem to vary inexplicably--even > if you > >>>>>>>> select another term and then come back to the same one, the > pulldown > >>>>>>>> list changes.)<Screen shot 2011-11-17 at 2.01.16 PM.png> > >>>>>>>> > >>>>>>>> Then select a discriminating relation and one of the > differentiae (not > >>>>>>>> the first one in the list): > >>>>>>>> <Screen shot 2011-11-17 at 2.01.44 PM.png> > >>>>>>>> > >>>>>>>> It now looks like this, right before I click Commit: > >>>>>>>> <Screen shot 2011-11-17 at 2.01.58 PM.png> > >>>>>>>> > >>>>>>>> As soon as I commit, both the genus and the differentia > change to other > >>>>>>>> terms (terms that weren't even in the pulldown lists!) > >>>>>>>> <Screen shot 2011-11-17 at 2.02.11 PM.png> > >>>>>>>> > >>>>>>>> When I tested earlier versions, I discovered that this is how > versions > >>>>>>>> from 2.1-b9 up to the present behave. > >>>>>>>> > >>>>>>>> Versions 2.1-b6 and 2.1-b7 had worse versions of this > >>>>>>>> problem--everything looked fine when you clicked Commit, but > if you > >>>>>>>> visited another term (by selecting it in the OTE) and then > returned to > >>>>>>>> the term for which you had created a cross-product, you would > find that > >>>>>>>> it was not the one you thought you'd saved. > >>>>>>>> 2.1-b6: looks ok when you commit, but if you select another > term (in the > >>>>>>>> OTE) and then return to the first one, the saved > cross-product is GONE. > >>>>>>>> 2.1-b7: looks ok when you commit, but if you select another > term (in the > >>>>>>>> OTE) and then return to the first term, the differentia you > selected has > >>>>>>>> changed to a different one. > >>>>>>>> > >>>>>>>> 2.00 behaved like the current version: the change in the > cross products > >>>>>>>> happens when you click Commit, not secretly behind the scenes. > >>>>>>>> > >>>>>>>> I also noticed that some versions (e.g., 2.1-b6) offer more > choices of > >>>>>>>> discriminating relations. I don't know whether that's good or > bad. In > >>>>>>>> most versions, when you try to create a cross-product for a > camphor > >>>>>>>> term, the only relations it shows in the pulldown list are > >>>>>>>> results_in_division_of and part_of. In 2.1-b6, you get a > longer list > >>>>>>>> that includes is_a, union_of, etc. > >>>>>>>> > >>>>>>>> > >>>>>>>> It seems to me that if this bug has existed since before 2008 > and hasn't > >>>>>>>> been mentioned again until this week, it does not qualify as a > >>>>>>>> show-stopper. I am adding this information to the bug report, > and will > >>>>>>>> tackle this bug after the 2.1 release, as time permits. > >>>>>>>> > >>>>>>>> Nomi > > -- Alexander D. Diehl, Ph.D. |