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[bioontology-support] Feedback

Natasha Noy noy at
Sun Jul 26 11:59:32 PDT 2009

Makes sense. I'll put in a feature request and we will try to figure  
out the best way to address this. Thanks for the suggestions!


On Jul 26, 2009, at 11:39 AM, Maryann Martone wrote:

> 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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