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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: Samson Tu <swt@stanford.edu>
Date: Wed, 23 Apr 2008 14:35:25 -0700
Cc: Samson Tu <swt@stanford.edu>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, <dan.russler@oracle.com>, <public-semweb-lifesci@w3.org>, <public-hcls-coi@w3.org>
Message-Id: <DA76850C-2740-4FC5-9FD1-57448F094E3C@stanford.edu>
To: "Elkin, Peter L., M.D." <Elkin.Peter@mayo.edu>

It's good that we separate the conceptual "layers" (views) from the  
logical/representation levels. My understanding of HL7 RIM classes is  
that they (at least classes like Observation) are meant to be  
*subclassed* into more specific domain classes. Templates/archetypes  
are constraints on (and hence describe subclasses of) these domain- 
specific classes. Instances of patient-specific HbA1c observations are  
also instances of Observation logically. HL7 experts among us can  
correct me if I am wrong.

Samson
-- 
Samson Tu                                                     email: swt@stanford.edu
Senior Research Scientist                               web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research 	phone: 1-650-725-3391
Stanford University                                          fax:  
1-650-725-7944





On Apr 22, 2008, at 1:07 PM, Elkin, Peter L., M.D. wrote:

> Dear Vipul and Dan,
>
> In order to not confuse the Ontology classification with First  
> Order / Second Order / Higher Order logics, we use Level 1  
> Ontologies to be domain independent (EAV just being a  
> representational mechanism for a logical system), level 2 Ontologies  
> are domain dependent (e.g. CDA), and level three contain defined  
> instances as well as class based definitions.  We have been able to  
> make these distinctions work across multiple projects.  If there is  
> a level zero I would suggest that Metaphysics or perhaps value  
> systems might be something that I have not seen well represented by  
> the upper level Ontologies with which I am familiar.
>
> I believe we need a final single formal representational schema  
> where constructions defined across Information Models and  
> Terminological Models can be validated.  This interlingua should be  
> defined from transforms from all other valid logical languages and  
> should empower all those SMEs familiar with any valid logical system  
> to work as they are comfortable.  In the end, that work product must  
> be validated through the common interlingua to ensure that meaning  
> is preserved and therefore we are not creating unrecognized ambiguity.
>
> With warm personal regards,
>
> Peter
>
> Peter L. Elkin, MD, FACP, FACMI
> Professor of Medicine
> Mayo Clinic College of Medicine
> Baldwin 4B
> Mayo Clinic
> (507) 284-1551
> fax:  (507) 284-5370
>
>
> From: Kashyap, Vipul [mailto:VKASHYAP1@PARTNERS.ORG]
> Sent: Tuesday, April 22, 2008 2:48 PM
> To: dan.russler@oracle.com
> Cc: Samson Tu; public-semweb-lifesci@w3.org; public-hcls-coi@w3.org;  
> Elkin, Peter L., M.D.
> Subject: Multi-layered Knowledge Representations for Healthcare (was  
> RE: An argument for bridging information models and ontologies at  
> the syntactic level)
>
> 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 Wednesday, 23 April 2008 21:36:33 GMT

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