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RE: Our white paper on Semantic Node Labeling in Clinical models

From: <Peter.Hendler@kp.org>
Date: Tue, 18 Sep 2012 07:12:56 -0700
To: ratnesh.sahay@deri.org
Cc: eric@w3.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
Message-ID: <OF2EAAA496.B80EBAB4-ON88257A7D.004D7362-88257A7D.004E16D2@kp.org>
I think I know what the difference is between our views.

I agree RDF might have been a better way to go then regular OO UML models. 
 But I'm addressing the state of the clinical modeling world for the past 
10 years or more.
The three main world wide clinical modeling systems in use are HL7 RIM, 
openEHR, and ISO 13606.
The vast majority (maybe even all) clinical models from standards 
organizations are OO, and most of them sometimes use SNOMED and often mess 
up the boundary between the 
intensional and extensional parts of the models. 

Our paper is to correct the current state of clinical modeling as it is 
and has been for many years.

It might be that these issues would be addressed differently if we were 
talking about a mixture of RDF and SNOMED.  But that's not how it is out 
in the world.

I wonder if there were mappings between the OO extensional parts of HL7 
CDA, openEHR, ISO 13606 and an RDF representation what new things could be 
done.
Probably a lot of useful new queries. 

We are pointing out the current state of the clinical modeling world of 
the three International standards currently used, and the mixing up of 
SNOMED with them.

Not the theoretical situation of mixing RDF and SNOMED which might be very 
useful and interesting.








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"Sahay, Ratnesh" <ratnesh.sahay@deri.org> 
09/18/2012 04:15 AM

To
Peter Hendler/CA/KAIPERM@KAIPERM
cc
<eric@w3.org>, "Deus, Helena" <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>
Subject
RE: Our white paper on Semantic Node Labeling in Clinical models






Hi Peter,
 
I agree that extensional (closed world clinical models) and intentional 
(SNOMED) models need a separate treatment. Developers (human)  or 
reasoners (machine) need a mechanism to understand their boundary and act 
appropriately. For example, below annotations in RED would help developers 
to interpret their scope of use. 
 
--OWL Manchester Syntax---
 
(1 ) DataProperty: effectiveTime
                Domain: ActLabObservation (*coming from HL7 RIM*)
                Range: xsd:dateTime
                Annotations: rdfs:label "local or extentional property"
 
 
(2) ObjectProperty: snomed:DirectSubstance
                Annotations: rdfs:label "Substance on which the lab 
procedure method directly acts"
                Annotations: rdfs:label "global or intentional property"
SubPropertyChain:
                snomed:DirectSubstance o snomed:HasActiveIngredient
 
However,  annotations (or lables) are reasoner-insensitive, so the 
separation and use of both type of models (extensional, intentional)  is 
entirely on a developer’s understanding.  IMO, to avoid “undesirable 
inferences” by “mixing-up” these two types of models (extensional, 
intentional), caution should be taken at a stage where alignments 
(subclass, equivalentClass, etc.) are created between them.  Also, there 
should be a guideline (for specific settings) about (1) when interfaces 
are required (i.e., reasoners); and (2) when only querying (SPARQL) is 
sufficient. This will help further on your proposal for SNL. Since long 
there has been a discussion on this [1,2] in the Semantic Web Community, 
still we need to see something concrete.
 
[1] B. Motik, I. Horrocks, R. Rosati, and U. Sattler, “Can OWL and Logic 
Programming Live Together Happily Ever After?” in International Semantic 
Web Conference, 2006, pp. 501–514. [Online]. Available: 
http://www.cs.ox.ac.uk/boris.motik/pubs/mhs06happily.pdf

 
[2] B. Motik, I. Horrocks, and U. Sattler, “Bridging the gap between OWL 
and relational databases,” J. Web
Sem., vol. 7, no. 2, pp. 74–89, 2009. [Online]. Available: 
http://www.cs.ox.ac.uk/ian.horrocks/Publications/download/2007/MoHS07a.pdf 

 
Regards,
Ratnesh 
 
 
From: Peter.Hendler@kp.org [mailto:Peter.Hendler@kp.org] 
Sent: 17 September 2012 22:20
To: Sahay, Ratnesh
Cc: eric@w3.org; Deus, Helena; kerstin.l.forsberg@gmail.com; 
LINMD.SIMON@mcrf.mfldclin.edu; meadch@mail.nih.gov; 
mscottmarshall@gmail.com; public-semweb-lifesci@w3.org
Subject: Our white paper on Semantic Node Labeling in Clinical models
 
This very clearly (to me at least) explains the problem and suggested 
solution to some of the problems we (Kaiser) see in clinical models. 

Wonder who agrees? 






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Received on Tuesday, 18 September 2012 14:14:00 GMT

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