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Re: seeks input on Study Data Exchange Standards An alternative approach

From: <Peter.Hendler@kp.org>
Date: Wed, 22 Aug 2012 10:28:13 -0700
To: conor-dowling@caregraf.com
Cc: david@dbooth.org, helena.deus@deri.org, kerstin.l.forsberg@gmail.com, LINMD.SIMON@mcrf.mfldclin.edu, meadch@mail.nih.gov, mscottmarshall@gmail.com, public-semweb-lifesci@w3.org, ratnesh.sahay@deri.org
Message-ID: <OF683986F5.17438B61-ON88257A62.005EA186-88257A62.005FF7CC@kp.org>
Well now you're going to make me admit more.
Although we are hoping to move to a RIM like clinical statement like SMIRF 
 (SMall Isolated RIM Fixed Model) as our enterprise clinical model, what 
most of our data is really in, ins Epic.
Which of course is a proprietary E.H.R. system and is of course an 
"extensional" model.

Now the drop down boxes where physicians pick diagnoses for example, are 
populated with local codes and local terms.  This is because doctors in 
general want to see the words they like, and not the "preferred name" of 
SNOMED or ICD9.

We maintain via our CMT (Convergent Medical Terminology) system a back end 
infrastructure.  CMT not only populates the Epic "master files" that 
determine what the user sees on the GUI but we also maintain all the 
mappings in a background database.  All of our local terms for procedures 
and diagnosis are mapped to SNOMED.  Our drugs are mapped to First 
Databank and I'm thinking probably also RxNorm.

So our whole system is at base, extensional based on Epic.  But, since we 
have diagnosis and procedures mapped to SNOMED, it give us an ability to 
use subsumption when ever we need to come up with a list of diagnosis or 
procedures for populating work flows, preference lists or even quality 
reporting or outcomes research.

We don't use any intensional ontology tricks in the "model".  We hope to 
eventually mirror our data in an HL7 RIM based SMIRF model.

But as it is now, the only ontology we map to in SNOMED, and pretty much 
the only reasoning we do is with the Clinical Findings and Procedures.

That said, it is a heck of a lot more useful and powerful than just using 
lexical searches to find these result sets.

Your issues about all the different ways you can divide a CCD (which is an 
HL7 RIM based structure) into it's RIM OO part and the SNOMED part are 
true issues that are not resolved.

I may have opinions on how I'd do it, but there are no agreed ways to 
converge on, and it would be hard to even state the rules if you were to 
come up with a single way.

The choice might be influenced by the actual model the E.H.R. system uses. 
If it has expected places for your "strawberry" then you would put it 
there, but if it doesn't you'd push it into a vocabulary space or even a 
post coordinated SNOMED expression.  But that's not an issue I want to 
tackle now.

I'd be happy to have people agree in the simple cases of a simple Dx, to 
use SNOMED in the "code" slot of the Observation, and label that node as 
being safe to use a SNOMED reasoner over the Clinical Findings hierarchy. 
This doesn't answer all the questions or cover all the things you need to 
do.  But it covers a heck of a lot of important cases, and it's simple and 
confined and easy.  An it might get many healthcare organisations started 
for the first time using any kind of subsumption or reasoning at all, 
without overwhelming them.


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Conor Dowling <conor-dowling@caregraf.com> 
08/22/2012 09:34 AM

To
Peter Hendler/CA/KAIPERM@KAIPERM
cc
david@dbooth.org, helena.deus@deri.org, kerstin.l.forsberg@gmail.com, 
LINMD.SIMON@mcrf.mfldclin.edu, meadch@mail.nih.gov, 
mscottmarshall@gmail.com, public-semweb-lifesci@w3.org, 
ratnesh.sahay@deri.org
Subject
Re: seeks input on Study Data Exchange Standards An alternative approach






Peter, 

how does Kaiser decide what level of coordination to use? Let me take 
RxNORM - do you use that for drugs? - does your OO/model record dosage, 
route etc or is that coordinated in the "what"? For SNOMED, do you stay 
clear of coordinated allergies (Allergic to Strawberries") and use two 
model fields 'Allergy' and (substance = strawberry) or do you use as much 
SNOMED coordination as you can? I suppose I'm asking, for each concept 
scheme, does Kaiser have a "profile" where you decide on coordination vs 
what's in the "model"? 

I had to do a lot of CCD stuff last year (opinion: a big messed up, going 
no-where hack) where the split of "model"/xml tags and terminologies/codes 
was never set and so you can lean on a terminology or the "model"/xml tags 
(see post). This is where I see the value in the split of concept scheme 
and clinical care vocabulary. It's not closed/open per se but in guidance 
or at least explicit recognition of multiple choices for expression beyond 
the obvious who-where-when.

On Wed, Aug 22, 2012 at 9:12 AM, <Peter.Hendler@kp.org> wrote:
My answer is not that there is anything intrinsically special about "what" 
vs the when why how etc. 

It is just based on what we actually do, and how SNOMED is. SNOMED is very 
good in the "what" of clinical models. 

On the one hand we're talking about all the possible things you could do, 
and on the other hand, the main real thing we really do is use SNOMED for 
"what". 

SNOMED is very strong in "Clinical Findings, Diseases, Observables, 
Procedures"  so those pre existing SNOMED hierarchies are in general 
"what" things. 




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Conor Dowling <conor-dowling@caregraf.com> 
08/21/2012 11:54 PM 


To
David Booth <david@dbooth.org> 
cc
Peter Hendler/CA/KAIPERM@KAIPERM, helena.deus@deri.org, 
kerstin.l.forsberg@gmail.com, LINMD.SIMON@mcrf.mfldclin.edu, 
meadch@mail.nih.gov, mscottmarshall@gmail.com, 
public-semweb-lifesci@w3.org, ratnesh.sahay@deri.org 
Subject
Re: seeks input on Study Data Exchange Standards An alternative approach








apologies if this is a tangent but why is what's identified as 
"extensional" particular to health-care? "Who" said/observed/found/acted 
"What", "When" and "Where" is surely a general notion. Does it need a 
health-care model or ontology? Yes, particular findings or observations or 
procedures can be of health but also of finance, indeed of most of 
life. "Constantine boiled his wife in 326" talks of who, what and when.  

Does Health-care need its own (closed-world) model for "observation" 
("kill method" == "boil") vs "finding" ("was the boiler") or "procedure" 
("dunk and hold down"). Just as we should avoid our own ontologies for 
demographics (a provider's address is not different than the address of a 
supermarket), shouldn't we avoid special handling for the likes of 
"observe", "find", "act" and leave each domain concentrate on its 
particular observations, findings et al? That is, SNOMED gets to be 
health-special but what here is called the "extensional model", that is so 
general (again, maybe I'm missing something), doesn't that belong with 
FOAF et al? 

On Tue, Aug 21, 2012 at 3:43 PM, David Booth <david@dbooth.org> wrote: 
On Tue, 2012-08-21 at 15:11 -0700, Peter.Hendler@kp.org wrote:
> [ . . . ]  Can you use RDF in a closed world way when ever you want, 
> or is it only safe when the model you're dealing with, like FHIR,
> really is known to be closed world?
> 
I think so, provided that you understand that you are making the closed
world assumption, i.e., that your results reflect only what you
*currently* know.

Almost every application makes the closed world assumption at some
point. 


--
David Booth, Ph.D.
http://dbooth.org/

Opinions expressed herein are those of the author and do not necessarily
reflect those of his employer.
Received on Wednesday, 22 August 2012 17:29:05 GMT

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