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

Hi Peter --

Agree --and I think I understand...:-).

Might we refer to them as "design-time" and "run-time"?  Or does that gloss over some of the important distinctions you are trying to point out?

Any materials on this topic you could distribute?

Thanks --

charlie
________________________________________
From: Peter.Hendler@kp.org [Peter.Hendler@kp.org]
Sent: Tuesday, August 21, 2012 12:22 PM
To: Mead, Charlie (NIH/NCI) [C]
Cc: eric@w3.org; helena.deus@deri.org; kerstin.l.forsberg@gmail.com; LINMD.SIMON@mcrf.mfldclin.edu; mscottmarshall@gmail.com; public-semweb-lifesci@w3.org; ratnesh.sahay@deri.org
Subject: RE: seeks input on Study Data Exchange Standards  An alternative approach

We are in fact talking about two different things.
If you are talking about how to more easily create new FHIR resources, and to assure their correct mapping to the RIM then my points are not relevant.


It is my view that clinical models can gain a lot of functionality by the addition of semantic web (RDF OWL and I even include SNOMED which is like a sub set of OWL).

For the actual use of these clinical models, we (Kaiser) have found it extremely useful to consider them as a clean separated model that has the largest part based on databases or OO (closed world standard stuff) but specifically designate some nodes, like the ones that would use SNOMED to represent diagnosis, findings, and procedures, to be considered as intensional logic that we use reasoners on.

For the purpose of assuring that the FHIR resources are correct and mapped correctly to the RIM, it may be good to move the entire model to RDF or OWL.  I haven't thought much about that task.

I was discussing the final use of such models.  In a FHIR resource for a diagnosis representation for example, there will be one node where you are allowed to use SNOMED to represent the diagnosis.  It is that one node that I would have labeled for the receivers (users) of that instance telling them they are free to use a SNOMED reasoner on that one part of the FHIR resource.

In future discussions we must be able to distinguish between which of these two problems we are discussing.

1  The problem you state which is related to the correct creation of models like FHIR
2  The problem I'm discussing which relates to the safe actual use of these models by clinical systems.

We could maybe call them the "authoring" or "use" problems respectively.









[cid:_2_115EDE7C115ED9A40059F8A388257A61]



NOTICE TO RECIPIENT:  If you are not the intended recipient of this e-mail, you are prohibited from sharing, copying, or otherwise using or disclosing its contents.  If you have received this e-mail in error, please notify the sender immediately by reply e-mail and permanently delete this e-mail and any attachments without reading, forwarding or saving them.  Thank you.





"Mead, Charlie (NIH/NCI) [C]" <meadch@mail.nih.gov>

08/21/2012 09:07 AM


To
        Peter Hendler/CA/KAIPERM@KAIPERM, "mscottmarshall@gmail.com" <mscottmarshall@gmail.com>
cc
        "helena.deus@deri.org" <helena.deus@deri.org>, "kerstin.l.forsberg@gmail.com" <kerstin.l.forsberg@gmail.com>, "LINMD.SIMON@mcrf.mfldclin.edu" <LINMD.SIMON@mcrf.mfldclin.edu>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>, "ratnesh.sahay@deri.org" <ratnesh.sahay@deri.org>, "Eric Prud'hommeaux" <eric@w3.org>
Subject
        RE: seeks input on Study Data Exchange Standards  An alternative approach







Hi Peter --

I haven't read the notes of today's discussion, but since I was the one that summarized the relationship between FHIR and OWL/RDF, I'd like to try and clarify things.  As it sounds like you know FHIR pretty well, let me start by saying that the original motivation behind seeing to what extent SW technologies were relevant to FHIR resource definition began with the observation that the initial proposed resource definition strategy for resources in general -- but particularly for the "core" resources that HL7 proposes defining and managing as balloted standards -- requires RIM mappings of resource elements.  The question that was put on the table several months ago was "Is there a computational grammar that we could use to define these mappings so that we can automatically process resource definitions to ensure that they are non-intersecting in terms of their overall semantics?"  In a really basic way, resources are identical to a SOA service inventory in which the design pattern of "service normalization" -- non-overlapping functional boundaries -- is critical for meaningful integration and composition of services.  The same is true of FHIR resources except at a purely static/informational rather than functional (as in the case of services) level.  The notion of having a computational grammar that defines a given resource's semantics also becomes important given that FHIR resources are expected to be deployed via REST interfaces, so trying to distinguish the boundary of one resource from another can't simply be done based on the semantics of the contract per se.  As we dug a bit deeply into this issue and figured out how to define these mappings in OWL and make them available at run-time as RDF, it became clear that being able to publish -- or at least have the publishable form be accessible through a single transform -- resource definition files in SW-friendly terms would be a very positive feature of FHIR (for those who were able to consume and leverage those definitions).  I think I understand and appreciate your Intensional/Extensional view and certainly agree that particularly if you're working in the world of SNOMED's expressivity, the approach makes sense.  However, the core motivation behind the use of SW technologies to model FHIR resources is simply to express the RIM mappings in a computational manner.  It is my personal -- and as yet unproven - hypothesis that this will also lead to a more stable wire format (an irrelevant issue with FHIR because one of its base tenants is a stable wire format (something which HL7 V3 messaging does not provide), but will have relevance if/when SW approaches to other HL7 specifications are applied.

Would it be possible for you to share any of your work -- ppt, white papers, etc. -- on your approach.  I think that the most positive aspect of this activity is that we're having a fairly new set of discussions within the HL7 community.

Thanks --

charlie
________________________________________
From: Peter.Hendler@kp.org [Peter.Hendler@kp.org]
Sent: Tuesday, August 21, 2012 11:47 AM
To: mscottmarshall@gmail.com
Cc: helena.deus@deri.org; kerstin.l.forsberg@gmail.com; LINMD.SIMON@mcrf.mfldclin.edu; Mead, Charlie (NIH/NCI) [C]; public-semweb-lifesci@w3.org; ratnesh.sahay@deri.org
Subject: Re: seeks input on Study Data Exchange Standards  An alternative approach

Sorry I didn't make the meeting but just looked at the minutes.

We (Kaiser) do use the Ontology features of SNOMED extensively and have a different take on how it should be done.

Specifically we would not advocate for example, putting FHIR in RDF or OWL.  What we've fount to be simple, useful, and very clean is to recognize the two different kinds of logic involved.
And keep them isolated to different parts of the model.

Intensional  (like OWL, Open World, Reasoners and inferences)
Extensional (like HL7 openEHR all Object Oriented models, all databases)

The base of a clinical model is always extensional Object Oriented, but there are nodes (attributes in the classes) that can take the data type Coded Data CD)

For example the "code" of an Observation class takes a code.  You can then designate that the code must be filled with only SNOMED or a SNOMED extension term that follows the same ontological scheme as SNOMED.

If you do this, then you can safely use a reasoner on the "code" for any Observation.

For example you can ask for codes that represent  "a disease with finding site lung structure with morphology fibrosis and disease process autoimmune".

Once you get this list of SNOMED codes then you iterate through them using Extensional logic (SQL) and then you have your list of patients.

This is the clear separation of the intensional and extensional parts of the model.  It is not the representation of the entire model in RDF or OWL.

We are just finishing a second white paper on a suggestion of how to extend this principle.  The basic idea is that clinical models, like HL7 are primarily at the base Extensional OO models and should not be represented as OWL or RDF.

But where it makes sense, you pick particular nodes like the "code" value of the Observation class, and then you add some meta information that indicates the following.

Intensional  TRUE/ FALSE   (the default is FALSE, you can not use a reasoner or SPARQL, this is an extensional OO node)
If TRUE then you supply the following additional meta tags.

logic  (for example OWL-DL, EL+ "same as SNOMED", RDF etc)
ontology  (for example SNOMED-CT)
post_coordinated_experessions_allowed  (TRUE/FALSE)
hierarchies (for example Clinical Findings, Observables)

Now any user or receiver of a model can scan the nodes for these tags.
If they find any with intensional="true" then they can inspect the other associated meta tags and know if they can use reasoners or SPARQL.

For the huge numbers of instances of these artifacts (messages or documents) that would be in the millions, you don't want to use reasoners but something faster like SQL. But for the nodes where it makes sense you can use OWL or some other reasoner dependent intensional logic.

In summary, it probably isn't a good idea to just move the model (for example FHIR) completely over to RDF or OWL.  Rather keep it an OO model but then use "Semantic Node Labeling" to designate particular nodes that you are allowed or expected to take advantage of SPARQL or OWL-DL or SNOMED





[cid:_2_1259C88C1259C4100056C87E88257A61]



NOTICE TO RECIPIENT:  If you are not the intended recipient of this e-mail, you are prohibited from sharing, copying, or otherwise using or disclosing its contents.  If you have received this e-mail in error, please notify the sender immediately by reply e-mail and permanently delete this e-mail and any attachments without reading, forwarding or saving them.  Thank you.

Received on Tuesday, 21 August 2012 16:56:00 UTC