W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2012

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

From: Conor Dowling <conor-dowling@caregraf.com>
Date: Wed, 22 Aug 2012 11:17:59 -0700
Message-ID: <CALfFB19n1WP+g7nVT_URRWe=aHR-ECmuqhkEwZqYk5NUXfnUJA@mail.gmail.com>
To: Peter.Hendler@kp.org
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
thanks Peter.

Just so I'm clear - and maybe getting too detailed for this discussion but
while I have you here - so the CMT (on NLM
here<http://www.nlm.nih.gov/research/umls/Snomed/cmt.html>)
defines selections and provides display names for SNOMED but do you have a
formal approach to the level of coordination?

Is severity always or never coordinated etc or is the approach "if it's in
CMT, it's used" and there's no formal definition of "this is for the model,
this is for the terminology". Or is Epic's model the determinant ie/ if
Epic has two slots - "allergin: Strawberry/ disorder: Allergy" - then you
don't coordinate and use separate terms from SNOMED but if Epic has one
slot - "Disorder type: Allergy to Strawberry" - then you coordinate?

Conor

On Wed, Aug 22, 2012 at 10:28 AM, <Peter.Hendler@kp.org> wrote:

> 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.
>
>
> *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.
>
>
>
>  *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*<http://www.caregraf.com/blog/so-much-choice-through-meaningful-use>).
> 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*<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.
>
>
>
> *
> 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.
>
>
>   *Conor Dowling <**conor-dowling@caregraf.com*<conor-dowling@caregraf.com>
> *>*
>
> 08/21/2012 11:54 PM
>
>   To
> David Booth <*david@dbooth.org* <david@dbooth.org>>
> cc
> Peter Hendler/CA/KAIPERM@KAIPERM, *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>, *
> meadch@mail.nih.gov* <meadch@mail.nih.gov>, *mscottmarshall@gmail.com*<mscottmarshall@gmail.com>,
> *public-semweb-lifesci@w3.org* <public-semweb-lifesci@w3.org>, *
> ratnesh.sahay@deri.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*<david@dbooth.org>>
> wrote:
> On Tue, 2012-08-21 at 15:11 -0700, *Peter.Hendler@kp.org*<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/* <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 18:18:27 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:13 GMT