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

From: Ogbuji, Chimezie <OGBUJIC@ccf.org>
Date: Thu, 10 Apr 2008 15:25:57 -0400
Message-ID: <2702D0EBA4F0A749968E52E8644184EA01DE9989@CCHSCLEXMB59.cc.ad.cchs.net>
To: "Oniki, Tom (GE Healthcare, consultant)" <Tom.Oniki@ge.com>, "Samson Tu" <swt@stanford.edu>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, rector@cs.man.ac.uk
cc: public-semweb-lifesci@w3.org, public-hcls-coi@w3.org

Thanks for that drill down, Tom.  It gives a good backdrop to call out
important distinctions

[[[
	* Clinical care - what we do to the patient based on our
assessments of the pathophysology of the patient
	*	I'm not sure if Alan is deliberately saying that this
"clinical care" level addresses actions taken *based on*
assessments/observations, but that assessments/observations themselves
*do not* fall into this category, but belong elsewhere (in the "record"
category below?) 
]]]

My understanding is that the distinction here is between the
characteristics of the patient (pathophysiology) and the clinical
actions that are part of the provision of care (diagnostic actions,
therapeutic actions, etc..).  Following this distinction, I would
consider an assessment to belong to this category, but I would not
consider an observation or a finding to fall in this category.  The
former is an action (or what BFO would call a Process), the latter are
data points recorded as a result of a clinical action.

[[[
	*	Here we have a "hypertension"
observation/finding/diagnosis. 
		*	A hypertension observation may be a subclass of
a more generic "observation" 
			*	It *makes reference to* the
"hypertension" of the pathophysiologic realm above, but is not
equivalent to that hypertension. 
]]]

Yes, this separation is critical IMHO.  Findings, diagnoses, measurement
data, and observations are sections of a medical record
(representational artifacts) that are *disjoint* from what they refer to
(in the pathophysiologic realm).

[[[
	* The record of that care and those assessments
	*	At this level, the hypertension record and the heart
rate record speak of RIM- or Archetype- or Clinical Element
Model-specific data structures. 
		*	It models from data capture/data exchange/data
retrieval use cases, which differs from the above levels 
			*	e.g., it allows a heart rate measurement
without a measurement location, even though in reality every heart rate
measurement is taken from some location. 
		*	Significantly, it is here that codes and code
systems are introduced -- the records reference these codes and code
systems, which as Alan says are "meta" to the pathophysiology realm
above, i.e., they're data structures that attempt to represent that
realm. 
]]]

I agree, however, with the caveat that I would group observations,
measurement data, and findings here (as a record of care and in the
realm of information models such as RIM, Archetypes, etc..).  The term
measurements is a bit ambiguous, so I wonder if what you had in mind was
the process (or action) of measurement or the resulting data.   

Chimezie (chee-meh) Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593
ogbujic@ccf.org 

 


________________________________

	From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Oniki, Tom
(GE Healthcare, consultant)
	Sent: Thursday, April 10, 2008 11:28 AM
	To: Samson Tu; Kashyap, Vipul; rector@cs.man.ac.uk
	Cc: public-semweb-lifesci@w3.org; public-hcls-coi@w3.org
	Subject: RE: An argument for bridging information models and
ontologies at the syntactic level
	
	

	It seems like we're having difficulty getting to a point where
we can see if we agree or not.

	Let me attempt to further a convergence by drilling down on what
Alan said earlier about the 3 levels of medicine, giving my
thoughts/interpretation:

	 

	* Pathophysiology - what we know about the patient

	*	A patient may have hypertension 

		*	The patient actually has to have some certain
"kind" or "subtype" of hypertension, e.g., "labile diastolic
hypertension" - no patient simply has "hypertension" 
		*	The patient's hypertension has a severity, e.g.,
"mild" 

			*	In this realm, the severity is mandatory
- *every* instance of hypertension has a severity 

		*	A patient has a heart rate, and the heart rate
has a value, e.g., "60 bpm" 

		*	In this realm, every patient has a heart rate
and every heart rate has a value, even if it's "0" 

	* Clinical care - what we do to the patient based on our
assessments of the pathophysology of the patient

	*	I'm not sure if Alan is deliberately saying that this
"clinical care" level addresses actions taken *based on*
assessments/observations, but that assessements/observations themselves
*do not* fall into this category, but belong elsewhere (in the "record"
category below?) 
	*	Regardless, I'm sure he's saying that
assessments/observations must be regarded separately from the
pathophysiology realm above. 
	*	For the sake of this drill-down, I'll assume
observations/measurements/assessments fall into this "clinical care"
category. 
	*	Here we have a "hypertension"
observation/finding/diagnosis. 

		*	A hypertension observation may be a subclass of
a more generic "observation" 

			*	It *makes reference to* the
"hypertension" of the pathophysiologic realm above, but is not
equivalent to that hypertension. 
			*	One may observe that a patient has
"hypertension", even though, as noted above, no patient actually has
"hypertension", but must have some particular subtype of hypertension.
(Or maybe at this level we would say the observation still has to be of
a certain type of hypertension, and it's only at the next level - the
record of care - that we're permitted to say the patient has generic
"hypertension"?) 

			*	We may also observe the severity of the
hypertension, i.e., a severity observation is an observation about the
hypertension's severity described above in the pathophysiology realm. 

			*	One can make a hypertension observation
without making a severity observation although, as stated earlier, in
the pathophysiologic realm, every hypertension has a severity. 

		*	Here we have a "heart rate measurement" 

		*	We measure the heart rate at a location, e.g.,
the left wrist 

			*	Every heart rate measurement has a
location - you can't measure the heart rate without measuring it at a
location 

			*	The value of the heart rate measurement
might not be the "true" value of the (pathophysiologic) heart rate, but
we accept it as an approximation 

	* The record of that care and those assessments

	*	At this level, the hypertension record and the heart
rate record speak of RIM- or Archetype- or Clinical Element
Model-specific data structures. 

		*	It models from data capture/data exchange/data
retrieval use cases, which differs from the above levels 

			*	e.g., it allows a heart rate measurement
without a measurement location, even though in reality every heart rate
measurement is taken from some location. 

		*	Significantly, it is here that codes and code
systems are introduced -- the records reference these codes and code
systems, which as Alan says are "meta" to the pathophysiology realm
above, i.e., they're data structures that attempt to represent that
realm. 

	 

	Look forward to your comments.

	 

	Tom

	 

	________________________________

		From: public-hcls-coi-request@w3.org
[mailto:public-hcls-coi-request@w3.org] On Behalf Of Samson Tu
	Sent: Wednesday, April 09, 2008 11:41 PM
	To: Kashyap, Vipul
	Cc: public-semweb-lifesci@w3.org; public-hcls-coi@w3.org
	Subject: Re: An argument for bridging information models and
ontologies at the syntactic level

	 

	On Apr 8, 2008, at 6:50 PM, Kashyap, Vipul wrote:

	
	
	

	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.

	 

	IMHO, codes don't represent classes in some information model.
An information model has classes like Observation, whose instances are
clinical statements made by some entity (person or machine). I think
information model is "meta" in the sense that its instances are
statements  (The observation that "John has diabetes") about something
that happens in the real world (the person named John has an instance of
Diabetes).  In BFO term, the observation is an instance of
information-content-entity, as opposed to an assertion about the John
instance of Person and an instance of Diabetes.

	
	
	

	 

	 The entire information structure - HL7 or Archetypes  - in
fact, is at a meta-level. 
	[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.

	 

	I don't understand how a class of HbA1c can be an instance of
the RIM Observation class.  I don't see how the Observation class having
the value field is the issue.

	 

	Samson


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Received on Thursday, 10 April 2008 19:27:23 GMT

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