Re: [BIONT] Latest Version of Parkinson's Disease Ontology (Molecular and Cellular Viewpoint)

On Sep 19, 2006, at 9:22 AM, Kashyap, Vipul wrote:

> In preparation of the BIONT Telecon today,
>
>
>
> The latest version of the Parkinson’s Disease Ontology in OWL is  
> available at:http://esw.w3.org/topic/HCLS/OntologyTaskForce/ 
> SeedOntology/
> OWL-DL axioms that model some of the “facts” identified by Bill Bug  
> are available at the bottom of:http://esw.w3.org/topic/HCLS/ 
> OntologyTaskForce/SeedOntology/SeedOntologyDetailedFollowup

Some quick comments:

> Reduced ubiquitin C-terminal hydrolase-1 expression levels in  
> dementia with Lewy bodies.
> Ubiquitin C-terminal hydrolase-1 subclass-of Protein
> Dementia subclass-of Disease i Do we need to model a class for  
> Patient?
> Introduce Axiom: (someValuesFrom has-disease Dementia) subclass-of  
> (hasValue expression-level reduced)

You need patient or at least organism, or you need to roll the  
organism into the relation.

Things which have diseases are organisms, so (someValuesFrom has- 
disease Dementia) is a subclass of say, organism.
Things which have expression levels, or amounts are, e.g. proteins so  
(hasValue expression-level reduced) is a subclass of say, protein.

One would think that organisms and proteins be disjoint classes. Two  
subclasses of two disjoint classes are also disjoint.

(someValuesFrom has-disease Dementia) subclass-of (hasValue  
expression-level reduced) is read as

All things which are (someValuesFrom has-disease Dementia) = some set  
of organisms are also
(hasValue expression-level reduced) = some set of proteins.

Which says that some organisms are proteins, which by the disjoint  
would be unsatisfiable.

So you need to make sure that the two halves of the subclass relation  
are of appropriate kinds. One way to do this would be to model  
something like "humans which have lower values of total expression of  
uclh1 measured in samples of their medulla oblongata". This is a  
subset of humans, and so the subclass relation you propose would say  
that one set of humans (those with dememtia) are a subset of another  
set of humans (those which have lower values of total expression of  
uclh1 measured in samples of their medulla oblongata).

Ok, got to go. Speak to you soon.

-Alan

Received on Tuesday, 19 September 2006 15:07:26 UTC