Re: Performance issues with OWL Reasoners

>>>>> "cm" == chris mungall <cjm@fruitfly.org> writes:

  cm> On Sep 14, 2006, at 10:26 AM, Phillip Lord wrote:

  >> This paper for example, managed to get the Gene Ontology and, I
  >> think, all of GOA into a DL form and reason over it in a, er,
  >> reasonable amount of time. S
  cm> InstanceStore is great!

  cm> I'd like to pose one question to you and the rest of the list

  cm> With InstanceStore, the genes and gene products are treated as
  cm> owl individuals - belonging to the ABox. 

If my memory serves me, this was the way that GO was encoded in the
example. Of course, it could have been encoded in a different way. 



  cm> However, the ontologically correct representation recognises
  cm> that p53 is the name of a universal that is instantiated in
  cm> trillions of cells, and not the name of an individual region of
  cm> DNA in an individual nucleus, and thus best represented in the
  cm> TBox. This is how we are thinking of presenting GO anntations in
  cm> OWL. This is obviously problematic from a practical POV.

Hmm, yes. I guess that what you really want here is some kind of
metaclass; p53 being an instance of tumour suppressor, and an
individual molecule being an instance of p53. 


  cm> It seems we need general patterns for transforming certain
  cm> subsets of TBoxes into ABoxes for the purposes of reasoning. Any
  cm> thoughts on how this should be done?

You do like to ask difficult questions!

I have to be honest, and say that I can't think of an obvious way of
doing this.  I guess it depends on what you need to query, when. If,
for example, you only ever need to dead with p53 as instance in one
set of queries and as a class in another, then you could do this
syntactically, by just having two representations of p53. Linking
between might be hard and would have to be at the hack level. 

If you need to refer to both at the same time, in the same query, then
I think you are stuffed. 

So, in short, no thoughts that you probably haven't already had for
yourself and are all fairly nasty. 

Phil

Received on Friday, 15 September 2006 10:54:58 UTC