[Pellet-users] A lot of descendant queries

[Alan Ruttenberg]

One problem with doing it the slow way is that memory consistently  
grows. Is there a reason that the call to getSubClasses need to  
allocate any long lived memory? So when doing this the way I suggest  
on the GO biological process ontology I eventually run out of memory  
when I don't think I should.

-Alan


On May 3, 2007, at 7:46 AM, Evren Sirin wrote:

> On 5/1/07 3:44 PM, Alan Ruttenberg wrote:
>> Hi,
>> I'm using pellet to compute inferred class level part_of  
>> relations  between classes in GO.
>> The way I do this is to load the ontology and then iterate over  
>> all  classes c asking for descendants of
>> (restriction part_of (some-values-from c))
>>
>> This takes quite a while. Is there a fast way to do this?
>>
> I cannot think of any straightforward way that is faster. So you  
> want to compute the mereological hierarchy similar to subsumption  
> hierarchy. I think the same strategy (and similar optimizations)  
> for computing the subsumption hierarchy would apply here. That is  
> you compute told part_of relations, do a top search for each  
> concept to find what it is part of and do a bottom search to find  
> what parts it has.  This strategy avoids many unnecessary tests and  
> reuses the previously found information effectively. A lot of the  
> code inside Pellet classifier could be reused but there is still a  
> fair amount of work that needs to be done to customize the  
> classification code for this purpose.
>
> Cheers,
> Evren
>> -Alan
>>
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