[Pellet-users] A lot of descendant queries

[Evren Sirin]

On 5/3/07 11:59 AM, Alan Ruttenberg wrote:
> 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? 
The getSubClasses function will insert the given concept into the class 
taxonomy and doing many calls to getSubClasses will probably eat up all 
the memory. It would be a good idea for us to put some kind of limit on 
how many (anonymous) concepts will be cached inside the taxonomy.

Cheers,
Evren
> 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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>>
>