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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 13:20:10 -0400
Message-ID: <1e89d6a40806031020r2fa8cf5cuc2448d93e6d53fbf@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 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 17:20:50 GMT

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