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Re: Revisiting structured datatypes was: Re: Revisiting AllDisjoint (was Proposed (parital) response to Ken Laskey and questions for WG)

From: Jim Hendler <hendler@cs.umd.edu>
Date: Tue, 15 Jul 2003 18:04:57 -0400
Message-Id: <p05200f61bb3a2899118d@[10.0.0.229]>
To: "Jonathan Borden" <jonathan@openhealth.org>, "webont" <www-webont-wg@w3.org>
Jonathan - specific questions about the NCI ontology seem to me to be 
out of scope for this WG unless they relate to LC comments -  For 
what it is worth, the developers of this ontology need these CDATA 
things this specific way (details can be provided elsewhere) and did 
not ask for structured datatypes in their LC comments [1].  (Also the 
new version of the ontology has defined all these as annotation 
types, so there's no semantic issue here per se)
  The WG agreed structured datatypes were desirable but that we would 
not be able to add them ourselves (in OWL) instead of in XSD or RDF 
[2] -- are you offering new evidence, preferably based on LC 
comments, that we should change our minds and reopen the issue?
  -JH


[1] 
http://lists.w3.org/Archives/Public/public-webont-comments/2003May/0068.html
[2] 
http://www.w3.org/2001/sw/WebOnt/webont-issues.html#I4.3-Structured-Datatypes


At 4:37 PM -0400 7/15/03, Jonathan Borden wrote:
Jim,

With all due respect, if we are going to modify OWL based upon the 
needs of the NCI Ontology (which *is* reasonable) then let's look at 
an example class definition:


[snip]

Pardon me, but this use of XML inside CDATA sections is a, to be 
blunt, horrible hack whose necessity raises serious concerns about 
the lack of structured datatypes in OWL. Since this seems essential 
to the ontology -- this idiom is repeated over and over -- I think 
that we need to readdress the issue of structured datatypes -- such 
use of 'XML' and I mean the quotes as the XML is inside CDATA 
sections !!! must raise a most serious interoperability issue.

This is aside from other properties such as <code> <id> and <CUI> 
which I suspect contains an identifier -- ought not these be 
resources i.e. URIs?

It looks to me as though these types of 'graphs' have all sorts of 
extra-RDF arrows between the nodes.

Jonathan

From: <mailto:hendler@cs.umd.edu>Jim Hendler

To: <mailto:jonathan@openhealth.org>Jonathan Borden ; 
<mailto:www-webont-wg@w3.org>webont
Sent: Monday, July 14, 2003 6:17 PM
Subject: Re: Revisiting AllDisjoint (was Proposed (parital) response 
to Ken Laskey and questions for WG)

At 6:05 PM -0400 7/14/03, Jonathan Borden wrote:
Different kinds of cancer, for example, are hardly disjoint: one 
person might have any number of different cancers -- really. If we 
are going to revisit anything that might actually improve something 
like GALEN, how about qualified cardinalities?

Jonathan


Jonathan - there are sets of diseases that do not/cannot co-occur, 
there are sets of genetic loci that are disjoint and others that 
arent, and, in fact, any reasoning system that is going to use any 
sort of medical ontology for classifying diseases (or patients, or 
lifestyles, or anything else) is going to have to represent these 
disjoints or the fact that its reasoning is complete and sound won't 
be worth much.  Sometimes these disjoints happen at a "high level" 
and our argument that there won't be many of them holds (Human v. 
non-human categorizes a lot of stuff), but sometimes these happen at 
a low level (all the different mammals are speciated in a disjoint 
way by nature, except a couple of odd cases like mules) and one would 
need to express them.   I'd bet you that there's a lot more disjoint 
statements that are needed for the NCI ontology [1] than QCRs - will 
you take that bet??
  -JH
p.s. And I'll just count the disjoint classes themselves, so I won't 
take unfair advantage of the N^2 to 1 that disjoints have over QCRs.

[1] http://www.mindswap.org/2003/CancerOntology/

----- Original Message -----

From: <mailto:hendler@cs.umd.edu>Jim Hendler
To: <mailto:www-webont-wg@w3.org>webont
Sent: Monday, July 14, 2003 5:32 PM
Subject: Revisiting AllDisjoint (was Proposed (parital) response to 
Ken Laskey and questions for WG)

I would like to take a moment to see what people think about having 
to reopen this issue (or possibly move forward over an objection):

In a conversation (non electronic) with Ken Laskey, who has again 
raised the issue of having an owl:allDisjoint construct (mirroring 
the allDifferent construct), I pointed him to Dan Connolly's [1] 
earlier response to this issue.  Ken indicated that he was not likely 
to accept this answer, and in conversation he brought up many use 
cases where this would be needed.  Basically, he disputes our 
contention that since this occurs in "class space" it is likely to be 
just a small number -- as he points out,  we already have a number of 
ontologies in OWL that are quite large (the NCI ontology and the 
GALEN ontology, are two examples).  In these ontologies, there are 
numerous cases where one would want to take a large set of classes 
(for example the different kinds of cancers) and make it explicit 
that some of these are disjoint (and thus others aren't necessarily) 
-- even though N is comparatively small, say 100 (remember the total 
number of classes in NCI is about 17000), this takes ~(N^2)/2 = 5,000 
(!!) OWL statements.
   Further, Ken points out that even in some of the smaller ontologies 
we've created, the number of classes and the number of disjoint 
classes can be almost identical (for example, military ranks are 
mutually disjoint within services, but not always between - someone 
cannot be an Army Lieutenant and and Army Captain, but there are rare 
cases where someone is "dual hatted" as an Army Colonel and a Navy 
Captain, for example).  Here's the odd thing -- the number of classes 
in the military ranks ontology would be about 50 (if one includes 
officers and non-officiers), which would require on the order of 1000 
disjoint statements --significantly dwarfing the size of the original 
ontology!
  Note that in none of these use cases are we talking disjoint unions 
per se (although I suppose one could create a workaround if one had a 
disjointunion construct).
  I think the N^2 problem in the size of the ontologies we're already 
seeing might be evidence to reopen this issue.  Alternatively, if 
there is a decent workaround, we might want to document that 
workaround and not add this construct.  We can also try to move 
forward over Ken's objection, although my preference would be to look 
for a way not to.

  -JH
p.s. Please note that this would NOT require any new semantics or any 
major new syntax - semantically we already have the ability to assert 
the pairwise disjuncts, and semantically this could be done using the 
same construct we created for allDifferent.


[1] 
http://lists.w3.org/Archives/Public/public-webont-comments/2003Jun/0038.html

--
Professor James Hendler				  hendler@cs.umd.edu
Director, Semantic Web and Agent Technologies	  301-405-2696
Maryland Information and Network Dynamics Lab.	  301-405-6707 (Fax)
Univ of Maryland, College Park, MD 20742	  *** 240-277-3388 (Cell)
http://www.cs.umd.edu/users/hendler      *** NOTE CHANGED CELL NUMBER ***


--
Professor James Hendler				  hendler@cs.umd.edu
Director, Semantic Web and Agent Technologies	  301-405-2696
Maryland Information and Network Dynamics Lab.	  301-405-6707 (Fax)
Univ of Maryland, College Park, MD 20742	  *** 240-277-3388 (Cell)
http://www.cs.umd.edu/users/hendler      *** NOTE CHANGED CELL NUMBER ***


-- 
Professor James Hendler				  hendler@cs.umd.edu
Director, Semantic Web and Agent Technologies	  301-405-2696
Maryland Information and Network Dynamics Lab.	  301-405-6707 (Fax)
Univ of Maryland, College Park, MD 20742	  *** 240-277-3388 (Cell)
http://www.cs.umd.edu/users/hendler      *** NOTE CHANGED CELL NUMBER ***
Received on Tuesday, 15 July 2003 18:05:05 GMT

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