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Re: An argument for bridging information models and ontologies at the syntactic level

From: Dan Russler <dan.russler@oracle.com>
Date: Sun, 27 Apr 2008 17:49:55 -0400
Message-ID: <4814F503.2030804@oracle.com>
To: Alan Rector <rector@cs.man.ac.uk>
CC: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, "Ogbuji, Chimezie" <OGBUJIC@ccf.org>, Dan Corwin <dan@lexikos.com>, "Oniki, Tom (GE Healthcare, consultant)" <Tom.Oniki@ge.com>, Samson Tu <swt@stanford.edu>, public-semweb-lifesci@w3.org, public-hcls-coi@w3.org
Hi Alan,

Your points are well made regarding the provenance of information and 
the information itself.

I captured this "assertion" as a point upon which to comment:

"My main contention is that the things that we put in medical records 
represent statements "ascribing" (or "not ascribing") characteristics 
and relationships to patients - i.e.
we are saying that the patient "_has_ a white count = 10,000" or that 
the patient "_has_ Diabetes".  (For diabetes we may also say that the 
patient "_does_not_have_ diabetes)..."

If we use your term "ascribing" to the more formal terms "proposition" 
(as statement which may or may not be true) and "assertion" (a 
proposition which is believed to be true), we can then apply the 
principles of formal analysis of propositions to "assertions" and other 
"propositions" found in the medical record. A differential diagnosis is 
a list of propositions; the result of a lab test in a medical record is 
normally an assertion. Of course, at the point where the author believes 
that one item in a differential diagnosis is "true," the proposition 
also takes on the characteristics of an assertion, just like the reult 
of the lab test.

Your point on provenence is a good one: "In each case there is a degree 
of inference - indicated by the fact that most information has to be 
"approved" before it gets into the record." In other words, we may make 
many assertions about patients in everyday speech, but only some 
assertions are allowed to be recorded in a medical record.

Teasing out these various stages in the evolution of how we come to 
think, speak, and record what we discover about patients is important 
before we get to the end-goal of improving the decisions we make 
regarding patients.

Dan

Alan Rector wrote:

> All
>
> I am coming in a bit late on this, but two points
>
> A)   I'd like to suggest that there are two, largely orthogonal, 
> dimensions (at least) being conflated:
>
> i) The evidence trail or "provenance" of information and our 
> consequent degree of belief/willingness to rely on that information
>
> ii) The information to be transmitted - and what information is 
> potentially available on each step of the process.
>
> The informational part (ii) is sketched from a slightly different 
> point of view in my Medinfo 07 paper (please use the corrected version)
> http://www.cs.man.ac.uk/%7Erector/papers/Whats-in-a-code/Whats-in-a-code-rector-corrected.pdf
>
> and in the paper that I shall present ar KR-MED 2008 in June, and is 
> currently being refereed for JAMIA. (Our preprint server is still 
> under construction, but I am happy to share the manuscript with 
> individuals interested.)  Hopefully it will be there by June.
>
> Although the fundamental problem is reasoning with clinical 
> information, the immediate problem for clinical systems is the 
> information itself, so I shall concentrate on that here.
>
> My main contention is that the things that we put in medical records 
> represent statements "ascribing" (or "not ascribing") characteristics 
> and relationships to patients - i.e.
> we are saying that the patient "_has_ a white count = 10,000" or that 
> the patient "_has_ Diabetes".  (For diabetes we may also say that the 
> patient "_does_not_have_ diabetes)
>
> Whether we enter the coded form in the medical record for "WBC=10,000" 
> or whether we enter "Diabetes" we are ascribing that condition to the 
> patient (at a given time, place, etc.)
>
> We may be basing this information on information about a sample, an 
> artifact (e.g. a Radiology study), a direct observation, or a 
> diagnostic inference.  In each case there is a degree of inference - 
> indicated by the fact that most information has to be "approved" 
> before it gets into the record.
>
> i) concerns the chain of evidence, long or short, and our systems 
> sometimes conflate the measurement and the statement of belief based 
> on that measurement (the "ascription").  However, when we go to reason 
> about it the reasoning is very different.  If we infer that the 
> patient has an elevated potassium we do something; if we think the 
> sample has been haemolized we do something else.  But no person "has" 
> a haemolised K+" although they may have the source from which "a 
> haemolised sample" was taken on which a measurement of K+ was performed.
>
> II) concerns what statements can convey information.  Since our 
> background information model (sometimes oddly called an "ontology") 
> says that all people at all times have a white count, there is no 
> point is saying "The patient has a white count" (although there is a 
> point in saying: "the patient has had a white count performed"). 
>
> All patients at all times have white counts, we may just be ignorant 
> of them. Therefore, simply saying that somebody _has_ a white count 
> tells us nothing we don't' know already and does not differentiate 
> them from other patients.   It conveys no information. To convey 
> information we have to say something about the white count, usually 
> its numerical value.  
>
> By contrast, "Diabetes" and "Cardiac Murmur" are both things that only 
> some people have only some of the time.  Simply to say that a patient 
> _has_ them conveys information because we don't know it already and 
> does differentiate them from other patients, or the same patient at 
> different times or as observed by different observers. 
>
> We tend to use the label "Situation" for the entity that reprsents a 
> patient at a time as observed by an observer (who records their 
> information) and "includes" as the property, so that, the appropriate 
> level for transforming between ontologies, codes, and information 
> models must take this into account.
>
> Note that "having diabetes" is different from "diabetes".  There is 
> different information to be conveyed about "diabetes" and about 
> "having diabetes" (or more precisely, ("situations having diabetes" - 
> or in our usual notation Situation THAT includes Diabetes).
>
> This approach deliberately makes it possible get the equivalences 
> between a finding
>
> "'_has_ WBC>=10,000" and what SNOMED has trditionally called an 
> "observable "'_has_ WBC' >= 10000'" as a test and value (range).
> And alows us to say of the same WBC that it is considered to be 
> 'elevated".
>
> The evidence chain for the statement that the WBC is elevated goes 
> back to the statement about the WBC being above 10,000 which in turn 
> goes back to the lab test etc.
>
> B) There is different information to be conveyed about the entity that 
> is being tested for - e.g. WBC - and the method of testing. Therefore 
> it makes sense for there to be separate entities for them at some 
> level in our modelling. (You can order a test, you can't order 
> somebody to have a WBC).  In the same way, the test result is clearly 
> different from the statement that it is valid for the patient.  We may 
> often elide this differences and encapsulate two or more entities for 
> purposes of a more efficient information system and/or a more 
> computationally tractable logical model, but they are real. We should 
> be clear when we are deliberately eliding different entities.
>
> I hope this is a useful intrusion.
>
> Regards
>
> Alan
>  
>
> -----------------------
> Alan Rector
> Professor of Medical Informatics
> School of Computer Science
> University of Manchester
> Manchester M13 9PL, UK
> TEL +44 (0) 161 275 6149/6188
> FAX +44 (0) 161 275 6204
> www.cs.man.ac.uk/mig <http://www.cs.man.ac.uk/mig>
> www.clinical-esciences.org <http://www.clinical-esciences.org>
> www.co-ode.org <http://www.co-ode.org>
>
>
>
>
> On 16 Apr 2008, at 20:16, Kashyap, Vipul wrote:
>
>>  
>>
>>     Ogbuji, Chimezie wrote:
>>
>>>     Dan,
>>>
>>>     I've very familiar with the SOAP model.  The primary motivation
>>>     for my questions about assessment had more to do with
>>>     distinguishing an action from data that is derived from it. 
>>>     This speaks directly to the problem of the 'anti-pattern' where
>>>     ontologies for medical records are built *directly* from models
>>>     that were designed with data-level concerns in mind and thus
>>>     semantically inconsistent (so called "information models").
>>>
>>>     The sense of assessment as used in this paper suggests that an
>>>     assessment is data (and thus appropriate to consider a
>>>     diagnosis), but consider that there are other senses of the word
>>>     and one in particular is "the act of judging or assessing a
>>>     person or situation or event".  In the latter case, an
>>>     assessment refers to the act.  I was simply trying to tease out
>>>     which of these Tom had in mind.
>>>
>>     <danR> It is true that in traditional lab department systems, the
>>     'data from the assessment' was modeled separately from the
>>     'assessment action.'  This is not exactly "wrong." However, it
>>     was noted that one cannot deliver a "numeric result" without
>>     restating the action that generated the result, e.g. serum WBC is
>>     the action and serum WBC of 10,000 WBcells/ml is the result. In
>>     physical sciences, it is considered good practice to always
>>     include the methodology of the action when describing the data.
>>     Accordingly, it is best practice in the science of healthcare to
>>     also report on the nature of the action itself at the same time
>>     as reporting on the data derived from the action. 
>>      
>>     [VK] It may be the case that one can model key properties that
>>     can enable the accurate assessment of the action.
>>     For instance, one could model things like the property being
>>     assessed, who is doing the assessment, the qualifiers of the
>>     assessment, etc. 
>>     The CEM approack followed by IHC seems to adopt this strategy.
>>     From what I can see, there doesn't appear a need to model all the
>>     aspects of an action.
>>      
>>     On the other hand, if there is indeed a need for more contextual
>>     information related to the action of performing the assessment,
>>     it is probably a good idea to
>>     model these two things separately and then link them via
>>     approporiate relationships modeling the context, but this likely
>>     to happen in an application specific manner.
>>      
>>     Cheers,
>>      
>>     ---Vipul
>>
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>>    
>>
>
>
Received on Sunday, 27 April 2008 21:58:40 GMT

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