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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: Adrian Walker <adriandwalker@gmail.com>
Date: Tue, 3 Jun 2008 15:30:21 -0400
Message-ID: <1e89d6a40806031230n6316fbc5xc94fb0b17a7b1e4b@mail.gmail.com>
To: dan.russler@oracle.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 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    Shared use is free

[2]  www.reengineeringllc.com/iblClient1.java

[3]  www.reengineeringllc.com/WikiSOA.pdf


Adrian Walker
Reengineering




On Tue, Jun 3, 2008 at 2:54 PM, Dan Russler <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    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>
> 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    Shared use is free
>>
>> Adrian Walker
>> Reengineering
>>
>>
>>
>>
>>
>> On Mon, Jun 2, 2008 at 9:25 AM, Dan Russler <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   (Flash video with
>>> audio)
>>>
>>> [2]
>>> 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    Shared use is free
>>>
>>> Adrian Walker
>>> Reengineering
>>>
>>> On Tue, Apr 22, 2008 at 5:25 PM, Dan Russler <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 19:30:59 GMT

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