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Re: Multi-layered Knowledge Representations for Healthcare (was RE: An argument for bridging information models and ontologies at the syntactic level)

From: Dan Russler <dan.russler@oracle.com>
Date: Mon, 02 Jun 2008 09:25:34 -0400
Message-ID: <4843F4CE.7030701@oracle.com>
To: Adrian Walker <adriandwalker@gmail.com>
CC: "Kashyap, Vipul" <VKASHYAP1@partners.org>, Samson Tu <swt@stanford.edu>, public-semweb-lifesci@w3.org, public-hcls-coi@w3.org, Elkin.Peter@mayo.edu
Hi Adrian,

Belief is at the core of an ontology, not at the perphery as you suggest.

For example, the belief that "Type 1 Diabetes" and "Type 2 Diabetes" 
both have a parent called "Diabetes" is a belief instantiated in the 
SNOMED hierarchy. Of course, this representation is frought with 
physiologic heresy (Type 1 and Type 2 Diabetes are only related 
physiologically through a symptom, i.e. hyperglycemia, not through 
common causal phisiologic pathways). However, many people will argue 
that the belief is "true."

Like most beliefs, one can argue that if the belief is traditional or 
pragmatic instead of strictly valid, it belongs in the ontology because 
it is accepted as "true" by many. However, it is impossible to create an 
ontology where everyone agrees with every belief stated. This situation 
isn't "wrong;" it is simply a fact of life in ontology development.

If you used a modifier as you suggest below, you would need to modify 
many of the hundreds of thousands of assertions represented in an 
ontology like SNOMED.

Dan

Adrian Walker wrote:

> Dan --
>
> You wrote
>
>   How does one bring belief into a model, e.g. realism, creationism, etc?
>
> One way of doing this is to write a layer of knowledge as rules in 
> executable English.  The rules can conclude things like
>  
>    "it is currently the view of US health professionals that..."
>
>    "a possibly useful hypothesis is that...."
>
> Then, English explanations can show the data and inferential evidence 
> for the conclusions. 
>
> There's a kind of Wiki for executable English that supports this.  
> It's online at the site below, and shared use is free.  The English 
> vocabulary is open, and so to a large extent is the syntax.  Some 
> background is in [1,2].
>
> Apologies to folks who have seen this before, and thanks for comments.
>
>                                                     -- Adrian
>                   
>
> [1] www.reengineeringllc.com/ibldrugdbdemo1.htm 
> <http://www.reengineeringllc.com/ibldrugdbdemo1.htm>   (Flash video 
> with audio)
>
> [2]  
> www.reengineeringllc.com/A_Wiki_for_Business_Rules_in_Open_Vocabulary_Executable_English.pdf 
> <http://www.reengineeringllc.com/A_Wiki_for_Business_Rules_in_Open_Vocabulary_Executable_English.pdf>
>
> Internet Business Logic
> A Wiki and SOA Endpoint for Executable Open Vocabulary English over SQL
> Online at www.reengineeringllc.com 
> <http://www.reengineeringllc.com>    Shared use is free
>
> Adrian Walker
> Reengineering
>
> On Tue, Apr 22, 2008 at 5:25 PM, Dan Russler <dan.russler@oracle.com 
> <mailto:dan.russler@oracle.com>> wrote:
>
>     Hi Vipul,
>
>     Peter is right that the term "EAV" is a data schema implementation
>     model, even though it maps directly to a classic proposition model
>     with subject, predicate, and object of the predicate.
>
>     Layer 0 then would be the most abstract layer consisting purely of
>     formal propositions. In this layer, some propositions may express
>     relationships between one or two other propositions, but
>     otherwise, no grouping of propositions (classes) nor inheritance
>     are characteristic of this layer.
>
>     Peter brings up a good point about the need to deal with belief
>     and values in the model. After all, an ontology is really a belief
>     system asserted by one or more people. How does one bring belief
>     into a model, e.g. realism, creationism, etc?
>
>     Regarding your note below on Layer 2...The question is whether
>     there are finer layers of distinction between level 1 and layer 2
>     (before one actually creates instances that apply to individual
>     patients)?
>
>     Dan
>
>
>     Kashyap, Vipul wrote:
>
>>     Dan and Peter,
>>      
>>     Based on conversations on this topic, there appears to be
>>     consensus of the need for multi-layered knowledge representation
>>     schemes
>>     for heatlhcare.  Will be great if we could brainstorm and come to
>>     some sort of consensus on these "layers". Would like to propose a
>>     strawman as enumerated below.
>>      
>>     Layer 0 = Entity - Attribute - Value or RDF triple based
>>     rerpesentations.
>>     Layer 1 = MetaClasses, e.g., Observation as in HL7/RIM
>>     Layer 2 = Classes in a Patient Model, Document Models, etc, e.g.,
>>     the class of HbA1c results for a class of Patients.
>>     Layer 3 = Data that are instances of Classes, e.g., a particular
>>     HbA1c result for a patient John...
>>      
>>     As per your e-mail, you seem to be suggesting that there is
>>     something in between Layer 1 and Layer 2. However, please note
>>     that Layer 2 consists
>>     of classes of assertions in the patient record and not instances.
>>      
>>     More reespnses are embedded in the e-mail below.
>>      
>>     <dan> With apologies to Peter in case I misrepresented your SOA
>>     presentation...Last week, Peter Elkin of Mayo Clinic delivered a
>>     presentation where he called the HL7 RIM a "first order ontology"
>>     because of the abstraction level of the RIM. He called the models
>>     derived from the RIM, e.g. analytic models, patient care document
>>     models like CDA, etc, "second order ontology" because they add a
>>     layer of concreteness to the abstractions of the RIM, i.e. an
>>     object with classCode of observation and moodCode of order
>>     becomes an "observation order object" with neither a classCode
>>     nor a moodCode. 
>>      
>>     [VK] Are there mathematical ways of describing these
>>     "derivations" for e.g., by using operations such as
>>     instantiations and generalizations/specializations.
>>      
>>     Also, in the above, it's not clear what the semantics of an
>>     "observation order" object is?
>>     For e.g., observations and orders are semantically distinct
>>     concepts, so in some sense an observation order class is likely
>>     to be unsatisfiable?
>>      
>>     The semantics of "moodCode" is not clear in Knowledge
>>     Representation terms. For instance, do various mood codes
>>     partition the instances of a class
>>     into subclasses that are possbily mutually disjoint?
>>      
>>      Finally, the coding systems themselves support the concreteness
>>     of a "third order ontology." For example, the SNOMED concept
>>     becomes an object itself without a code attribute, moodCode
>>     attribute, or classCode attribute, e.g. a WBC order. />
>>     [VK] One way of looking at a Snomed code is that it defines a
>>     class (e.g., blood pressure) of all the instances of blood
>>     pressure readings which would imply that it belongs to Layer 2 as
>>     defined above? 
>>
>>>             <dan> see above for the "first order to third order
>>>             model." Your metaclass looks like Peter's "first order
>>>             ontology." However, your "instances" get introduced too
>>>             early...your "instances" point to actual medical record
>>>             assertions, and Peter's model suggests that there is
>>>             more "in between." In Peter's model, the actual medical
>>>             record assertion would be an instance of his "third
>>>             order ontology." />
>>>             [VK] Agree. As per the layering introduced above,  Layer
>>>             2 would correspond to classes of assetions and Layer 3
>>>             would correspond to actual instances or assertions.
>>>
>>>              <dan> I completely agree that the HL7 RIM is one level
>>>             more "concrete" than the earlier EAV models. The EAV
>>>             model represents the ultimate in abstraction, similar to
>>>             RDF triples. Perhaps Peter would be more correct to say
>>>             that EAV is a "first order ontology" and that the HL7
>>>             RIM is a "second order ontology." />
>>>              
>>>             [VK]  Agree: As per layering introduced abiove,  The
>>>             EAV/RDF triples layer could be layer 0, and the HL7/RIM
>>>             layer could be layer 1
>>>
>>>              
>>>             Look forward to further brainstorming and feedback on this.
>>>              
>>>             Cheers,
>>>              
>>>             ---Vipul
>>>
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Received on Monday, 2 June 2008 13:26:52 GMT

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