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RE: Performance issues with OWL Reasoners => subclass vs instance-of

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Thu, 14 Sep 2006 20:12:30 -0400
Message-ID: <2BF18EC866AF0448816CDB62ADF6538104C16460@PHSXMB11.partners.org>
To: "chris mungall" <cjm@fruitfly.org>, "Phillip Lord" <phillip.lord@newcastle.ac.uk>
Cc: <semantic-web@w3.org>, <public-semweb-lifesci@w3.org>

> 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

[VK] Actually this gets to the heart of one of the design issues identified by
the BIONT Task Force in designing the Parkinson's Disease Ontology.
Is a given gene a subclass or an instance-of a general "Gene" class.

http://esw.w3.org/topic/HCLS/OntologyTaskForce/DesignIssues (point number 2)

An initial draft of the ontology is available at:


Obviously, if mapping into instances gives better performance for a given set of
inferences, that might be the basis of choosing the instance-of relationship.
Towards this end I have the following questions for Phil:

1. What are the set of Abox inferences implemented in the GO example?
2. What would be the corresponding set of TBox inferences implemented if the
design choice proposed by Chris was adopted, i.e., p53 is a subclass of Gene
(assuming a general "Gene" class)
3. What are the performance and scalability implications of (1) vs (2)
4. What are the expressiveness implications of (1) vs (2), i.e., can we express
some statements using subclass-of based modeling which are not possible using
instance-of modeling; or vice versa....

Look forward to a good use case illustrating the above and discussing its
possible consequences.


Received on Friday, 15 September 2006 00:12:52 UTC

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