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

From: Samson Tu <swt@stanford.edu>
Date: Tue, 8 Apr 2008 12:18:21 -0700
Cc: Samson Tu <swt@stanford.edu>, public-semweb-lifesci@w3.org, public-hcls-coi@w3.org
Message-Id: <3E504E9E-1689-43F2-8F26-4322DFBC4AB4@stanford.edu>
To: Alan Rector <rector@cs.man.ac.uk>
Alan,

I agree completely. The observations and orders we capture in the  
information model are clinical statements that are meta to the actual  
objects and processes in the world. The codes in the statements are  
symbols representing classes in the ontology that is the underpinning  
of the terminological codes.

A clinical trial ontology, IMHO, can make reference to the information  
model because that's the repository of data about a subject. For  
example, to make an eligibility criterion like "the patient has not  
had medication X in the past two years" computable, we have to query  
the medical record (or an approximation of it, like a vMR) for the  
presence of that medication (and its subtypes).

Samson

On Apr 8, 2008, at 1:39 AM, Alan Rector wrote:

> Samson, Vipul, All
>
> I saw this by accident and have not been involved in the main  
> discussion - so excuse the intron.  However, the issue of the  
> relation between ontologies and health records is close to my  
> heart.  There are papers about it at both KR-MED 2006 and Medinfo  
> 2007, the KRMed paper due to appear in Applied Ontologies RSN.Both  
> papers are available from my web site http://www.cs.man.ac.uk/ 
> ~rector.  An expanded and clearer version of the KR-MED paper will  
> be available as soon as the mills of the gods grind at AO
>
> 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.  The entire information structure - HL7 or  
> Archetypes  - in fact, is at a meta-level.  It makes sense to talk  
> about a form on a patient on which the code or value for body- 
> temperature is missing; it does not make sense to talk about a  
> patient without a body temperature, even if it is ambient.  It makes  
> no sense to talk about the class of hypertensive patients except  
> those that fall into some subclass of hypertension, 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.
>
> 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.  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
>
> 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.
>
> Regards
>
> Alan
>
> On 7 Apr 2008, at 21:45, Samson Tu wrote:
>>
>> On Apr 3, 2008, at 7:56 PM, Kashyap, Vipul wrote:
>>>
>>>
>>> OK, we disagree on this point. I'd just point out that, if you are  
>>> interested in working with HL7 RIM or BRIDG, you have a conceptual  
>>> mismatch with them.
>>> [VK] I do not view it as a conceptual mismatch as I can get Snomed- 
>>> CT the terminology by specifying a transformation on Snomed-CT the  
>>> information model.
>> Perhaps you can elaborate on your idea of SNOMEDCT the information  
>> and what kind of transformations are involved to get SNOMEDCT the  
>> terminology.
>>
>>>
>>> If your Acute MI is a subclass of Observation/Problem, then  
>>> instances of "Acute MI" class are observations of Acute MI, not  
>>> instances of the disease MI. An "observation" does not have  
>>> severity, location, and so on. You lose the ability to talk about  
>>> properties of the things in the world.  An information model  
>>> refers to codes not because of implementation concern, but because  
>>> component parts of informational entity are also informational  
>>> entities, IMHO.
>>> [VK] Would like to separate the issue of incorrect modeling from  
>>> the issue of including class analogs of terminological codes into  
>>> an information model in general.
>>> As far as severity, location, etc are concerned, these could be  
>>> implemented as qualifiers to the observations as proposed in the  
>>> Clinical Element Model approach by Stan Huff et. al.
>>> That said, the issue is not that of accuracy in modeling as I used  
>>> Acute MI as an example. was proposing an information architecture  
>>> where we create a common framework to model and perform inference  
>>> on information models and terminologies.
>>>
>> Several years ago, I tried to formulate the Clinical Element Model  
>> as an ontology without any success. I came to see it as a very  
>> flexible data structure for encoding information. If you have  
>> better luck formulating it as an ontology, I'd like to know about it.
>>
>> Thank you.
>>
>> Samson
>
> -----------------------
> Alan Rector
> Professor of Medical Informatics
> School of Computer Science
> University of Manchester
> Manchester M13 9PL, UK
> TEL +44 (0) 161 275 6149/6188
> FAX +44 (0) 161 275 6204
> www.cs.man.ac.uk/mig
> www.clinical-esciences.org
> www.co-ode.org
>
>
Received on Tuesday, 8 April 2008 19:19:21 GMT

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