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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: Mon, 2 Jun 2008 10:43:23 -0400
Message-ID: <1e89d6a40806020743u5b100e46kc1938bd4dc358f1b@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 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 Monday, 2 June 2008 14:44:03 GMT

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