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[bioontology-support] Feedback

Maryann Martone maryann at
Sun Jul 26 11:39:28 PDT 2009

I think they probably are obsolete terms (try "maternal").  I didn't  
check them against the OBO file (I use Bioportal for my checking), but  
that was my next step.  I notice that they show up in the deprecated  
class in NIFSTD which imports PATO.  So I would say some sort of  
indication that this is an orphan or deleted class would be useful so  
we don't annotate to it (or report it as a bug!).

On Jul 26, 2009, at 11:34 AM, Natasha Noy wrote:

> Hmm...
> I played around with it a bit and it appears that the terms that  
> exhibit this behavior are obsolete terms that do not have any  
> parents defined. Here is an example:
>> [Term]
>> id: PATO:0000075
>> name: threshability
>> is_obsolete: true
> Two question: what are the terms that you observed this for? If you  
> check them against the OBO file, do they have the same structure?
> Second, what should we do with these terms that do not have any  
> parents defined. Should we not index them at all? If we index them,  
> what happens when you click in the search result? Maryann, what  
> would be useful?
> Natasha
> On Jul 26, 2009, at 11:16 AM, admin at wrote:
>> Name : Maryann Martone
>> Email : mmartone at
>> Comment:
>> I'm having trouble viewing the tree structure of PATO in the left  
>> navigation bar.  When I try to view a term from PATO, it displays  
>> the term in the right panel, but at the left, it only displays the  
>> root term "quality".  If I try to go to a term directly from the  
>> left search box, it still doesn't display the tree.
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at

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