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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 13:15:07 -0400
Message-ID: <48442A9B.4040305@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,

I like your use case...we need better tools for CQI of ontologies...Dan

Adrian Walker wrote:

> Hi Dan --
>
> Thanks for your thoughts about this. 
>
> You wrote...
>
> 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.
>
> Actually, it seems that reasoning in executable English over SNOMED 
> and other ontologies could be a useful way of addressing your point that
>
> ...it is impossible to create an ontology where everyone agrees with 
> every belief stated.
>
> The executable English can be used to say things like
>
>    "according to SNOMED this-type1 and this-type2 are closely related 
> but not everyone agrees"
>
> Users can then get English explanations showing the pertinent entries 
> in SNOMED, and showing who disagrees and why and for what purposes.
>
> How does that sound?
>
> If it's of interest, we can put up an example at [1] that folks can 
> run using browsers.  Scalability comes from automatically generating 
> and running SQL from the executable English.  The results are still 
> explained in English.
>
>                                         Cheers,  -- Adrian
>
> [1]  Internet Business Logic
>       A Wiki and SOA Endpoint for Executable Open Vocabulary English 
> over SQL and RDF
>       Online at www.reengineeringllc.com 
> <http://www.reengineeringllc.com>    Shared use is free
>
> Adrian Walker
> Reengineering
>
>
>
>
>
> On Mon, Jun 2, 2008 at 9:25 AM, Dan Russler <dan.russler@oracle.com 
> <mailto:dan.russler@oracle.com>> wrote:
>
>     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 17:17:19 GMT

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