- From: Alan Ruttenberg <alanruttenberg@gmail.com>
- Date: Tue, 19 Sep 2006 10:59:28 -0400
- To: Vipul Kashyap <VKASHYAP1@PARTNERS.ORG>, systemsbiology <public-semweb-lifesci@w3.org>
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