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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: Tue, 03 Jun 2008 16:39:01 -0400
Message-ID: <4845ABE5.7040105@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,

Extending the client stub would be another way to expose a web service. 
Good thought.

Dan

Adrian Walker wrote:

> Hi Dan --
>
> Thanks for your quick reply.  You wrote....
>
> I'm sure someone would have to write the EJB...for teaching, it would 
> be nice to expose a web service that a student could incorporate into 
> a web service orchestration routine over the internet.
>
> Yes, that would be one approach. 
>
> Another way is to let the IBL system [1] combined with SQL provide the 
> business logic, and to extend the IBL client stub [2] as needed to 
> expose a findable web service.
>
> Slide 17 of [3] illustrates this.
>
> How does that sound?
>
>                                  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
>
> [2]  www.reengineeringllc.com/iblClient1.java 
> <http://www.reengineeringllc.com/iblClient1.java>
>
> [3]  www.reengineeringllc.com/WikiSOA.pdf 
> <http://www.reengineeringllc.com/WikiSOA.pdf>
>
>
> Adrian Walker
> Reengineering
>
>
>
>
> On Tue, Jun 3, 2008 at 2:54 PM, Dan Russler <dan.russler@oracle.com 
> <mailto:dan.russler@oracle.com>> wrote:
>
>     Looks interesting. I'll keep this in mind.
>
>     Although I'm sure someone woud have to write the EJB...for
>     teaching, it would be nice to expose a web service that a student
>     could incorporate into a web service orchestration routine over
>     the internet.
>
>     Maybe this is a potential student project?
>
>
>     Dan
>
>     Adrian Walker wrote:
>
>>     Hi Again Dan --
>>
>>     You wrote:   I like your use case...we need better tools for CQI
>>     of ontologies..
>>
>>     Please feel free to use the Internet Business System [1] for this
>>     and other purposes.
>>
>>     As mentioned, shared use is free.  We will be happy to assist.
>>
>>                                Best regards,  -- 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
>>     Phone: USA 860 830 2085
>>
>>     On Mon, Jun 2, 2008 at 1:15 PM, Dan Russler
>>     <dan.russler@oracle.com <mailto:dan.russler@oracle.com>> wrote:
>>
>>         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 Tuesday, 3 June 2008 20:40:16 GMT

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