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RE: An argument for bridging information models and ontologies at the syntactic level

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Tue, 8 Apr 2008 21:50:04 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D1240236D4E6@PHSXMB20.partners.org>
To: "Alan Rector" <rector@cs.man.ac.uk>, "Samson Tu" <swt@stanford.edu>
Cc: <public-semweb-lifesci@w3.org>, <public-hcls-coi@w3.org>
Fundamentally, the only interpretation that works is to regard codes as being
"meta" to the ontology.  I.e. the individuals in the ontology are things in the
conceptualisation of the world - cases of diabetes, people, livers, etc. -
individual codes represent classes in the ontology.  
[VK] Agree. Codes represent classes in some ontology or information model.
 The entire information structure - HL7 or Archetypes  - in fact, is at a
[VK] Agree with this. In particular, the HL7/RIM has a very confusing
construction. It could be viewed as a meta-model but then it also has fields to
store patient data,
For e.g., one may view a class of lab values, say HbA1c as an instance of the
RIM Observation class (making it a meta-class), however, the RIM Observation
class also
has the value field for the value of those labs and is in some sense a
multi-layered representation, which is probably why it is so confusing.
It makes no sense to talk about the class of hypertensive patients except those
that fall into some subclass of hypertension, 
[VK] Wouldn't this translate to the difference between hypertension and its
 but it makes perfectly good sense to talk about the code for hypertension but
not its subcodes as being a valid filler for, say, a heading. 
[VK]  Do you mean the code associated with the class defined by the difference
of hypertension and the subclass of hypertension referred to above?
I thought you proposed a transformation between these two representations in
your KR-MED paper. Looks like I am missing something here.
Look forward to further clarification.

	We are again in the process of doing such representations for both OCRe
and two commercial collaborations.  One thing I feel confident about from this
work is that a single level representation of the ontology of disorders of
patients and the information structures about them, including codes, does not
work.  We can often get away with approximations which ignore the difference for
specific applications. Because our tools for handling multi-layer
representations are poor, we sometimes have to, but the problem is fundamental.
	it isn't even a question of what formalism one uses.  
	[VK] I agree that the key issue is that of multi-layered representations
and one way could be to engineer a crisp layering. For instance, disallow
representation of lab values in the meta-model layer and represent them as
instances of the HbA1c class in the information
	model layer. As far as multuple applications are concerned, one could
define transformations to produce application specific data models. Am not sure
how this approach would work and any feedback on this would be useful.
	 Medicine involves
	* Pathophysiology - what we know about the patient
	* Clinical care - what we do to the patient based on our assessments of
the pathophysology of the patient
	* The record of that care and those assessments
	[VK] Curious to understand why you distinguish between record of
clinical care and clinical care? Is it because of versioning and provenance?
	Decisions often involve all three levels.  Our actions may be based on
whether or not a particular piece of information is present in teh record , our
uncertainty about its value , or is value. 

	As far as SNOMED-CT goes, to a first approximation, the distributed form
can be viewed as being "codes" in this sense and should not be taken as an
"ontology" the codes are individuals representing classes of patients.  The
"Ontology" is the underlying "stated form" which we rarely see. Unfortunately,
some of the things people try to do with SNOMED ignore this point, and the
documentation on the issue is confusing at best.
	[VK] Agree with this, The distinction between SNOMED-CT the underlying
ontology and SNOMED-CT the terminology (collection of codes) is important and
one must not confound one with the other. 

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Received on Wednesday, 9 April 2008 01:52:31 UTC

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