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Re: Performance issues with OWL Reasoners

From: chris mungall <cjm@fruitfly.org>
Date: Thu, 14 Sep 2006 12:15:53 -0700
Message-Id: <8D620F80-D2E8-4239-A48F-600326C5FE7B@fruitfly.org>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, <semantic-web@w3.org>, <public-semweb-lifesci@w3.org>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>


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. So scalability to 10's of thousands of T-box and 100's
> of thousands of A-Box's is possible.
>
> http://www.cs.man.ac.uk/~dturi/papers/instancestore2.pdf

InstanceStore is great!

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

In non-biological applications, there is a general assumption that  
the TBox is relatively limited and the ABox is potentially huge, and  
algorithms are built with that in mind.

With InstanceStore, the genes and gene products are treated as owl  
individuals - belonging to the ABox. However, the ontologically  
correct representation recognises that p53 is the name of a universal  
that is instantiated in trillions of cells, and not the name of an  
individual region of DNA in an individual nucleus, and thus best  
represented in the TBox. This is how we are thinking of presenting GO  
anntations in OWL. This is obviously problematic from a practical POV.

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

Chris

>
> The DL reasoners are much better than they used to be -- in the good
> old days, when the world was young, you could get most DL reasoners
> to eat your CPU on a 10 term ontology. Nowadays, it's fairly hard to
> do this.
>
> Phil
>
Received on Thursday, 14 September 2006 19:15:56 UTC

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