RE: An HL7 RIM navigation language based on SPARQL?

The RIM is not the whole story.  The MIF is.
________________________________________
From: Michael Miller [Michael.Miller@systemsbiology.org]
Sent: Tuesday, October 02, 2012 2:05 PM
To: Peter.Hendler@kp.org; me@jerven.eu
Cc: eric@w3.org; helena.deus@deri.org; kerstin.l.forsberg@gmail.com; LINMD.SIMON@mcrf.mfldclin.edu; Mead, Charlie (NIH/NCI) [C]; mscottmarshall@gmail.com; public-semweb-lifesci@w3.org; ratnesh.sahay@deri.org
Subject: RE: An HL7 RIM navigation language based on SPARQL?

hi peter,

interesting question and discussion.  i definitely agree with david's take on the question that the physicians should have a nice GUI to separate them from the details.

RIM is modeled with UML (tho it is somewhat odd that viseo is used to visualize the models).  there is an OMG specification[1] that describes a way to map from UML to OWL/RDF and there are always less rigorous formulations that would do, along the lines of transforming a database schema to RDF.

michael

Michael Miller
Software Engineer
Institute for Systems Biology

[1] http://www.omg.org/spec/ODM/1.0/

From: Peter.Hendler@kp.org<mailto:Peter.Hendler@kp.org> [mailto:Peter.Hendler@kp.org<mailto:Peter.Hendler@kp.org>]
Sent: Tuesday, October 02, 2012 10:54 AM
To: me@jerven.eu<mailto:me@jerven.eu>
Cc: eric@w3.org<mailto:eric@w3.org>; helena.deus@deri.org<mailto:helena.deus@deri.org>; kerstin.l.forsberg@gmail.com<mailto:kerstin.l.forsberg@gmail.com>; LINMD.SIMON@mcrf.mfldclin.edu<mailto:LINMD.SIMON@mcrf.mfldclin.edu>; meadch@mail.nih.gov<mailto:meadch@mail.nih.gov>; mscottmarshall@gmail.com<mailto:mscottmarshall@gmail.com>; public-semweb-lifesci@w3.org<mailto:public-semweb-lifesci@w3.org>; ratnesh.sahay@deri.org<mailto:ratnesh.sahay@deri.org>
Subject: Re: An HL7 RIM navigation language based on SPARQL?

It's because clinicians will balk at the URIs.  The DSL would have the same logic exaclty but all resource names and URIs would have to be replaced with obvious business names.
Clinicians complain if they don't see exactly what they want it called.

How do I know?  I've been working on Kaiser's CMT (Convergent Medical Terminology) system since 1995.  Our clinicians will not settle for SNOMED preferred names, nor ICD names.  They want their own familiar terms.  We have a local clinician interface term for everything.  In the background we map to SNOMED.

You can get them to understand triplets, but you can't make them look at Resource names or URIs.





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Jerven Bolleman <me@jerven.eu<mailto:me@jerven.eu>>

10/02/2012 10:37 AM

To

Peter Hendler/CA/KAIPERM@KAIPERM

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Subject

Re: An HL7 RIM navigation language based on SPARQL?







Hi All,

Is SPARQL to difficult to teach to clinicians? I personally think its not. What is difficult to explain is the data model (especially a HL7 compatible one.)

Explaining a simple select once they understand triples is easy.

I love_my work = simple sentence = subject predicate object
<ch.linkedin.com/in/jervenbolleman<http://ch.linkedin.com/in/jervenbolleman>> <http://dictionary.reference.com/browse/love> <http://beta.sparql.uniprot.org<http://beta.sparql.uniprot.org/>> = replace words by uri's

<ch.linkedin.com/in/jervenbolleman<http://ch.linkedin.com/in/jervenbolleman>> <http://dictionary.reference.com/browse/love> ?thingHeLoves = uri's by a variable starting with a ?

Wrap in select

select
?thingHeLoves
where
{
      <ch.linkedin.com/in/jervenbolleman<http://ch.linkedin.com/in/jervenbolleman>> <http://dictionary.reference.com/browse/love> ?thingHeLoves
}
find
<http://beta.sparql.uniprot.org<http://beta.sparql.uniprot.org/>>

This basic concept is easily explainable in an afternoon. You will need at least as much time to introduce any DSL as well.
The problem remains the HL7 data model. If you can explain that to anyone in an afternoon you are my hero ;) and your DSL will need to fight that as well. In which case it would be better to spend you time rewriting the HL7 data model into something that matches a clinicians model of his world. You would need reasoning and/or rules to do so.

The benefit of sparql will be the capability to work with excell and or tab delimited files that the clinician already has. Using for example bio-table and the SPARQL 1.1. service keyword.

Regards,
Jerven

PS. I couldn't find an URI to identify my wife so had to fudge the example ;)
On Tue, Oct 2, 2012 at 7:15 PM, <Peter.Hendler@kp.org<mailto:Peter.Hendler@kp.org>> wrote:
Mainly for Charlie and Eric but anyone who knows RIM.

There has been talk off and on for ever about a Domain Specific Language for navigating RIM like graphs of data.  Seems to me SPARQL can already do that.
But SPARQL is too much to teach clinicians.  So you could have a RIM specific DSL that is like a RIMQL.  It could be nothing more than a thin layer on top of SPARQL.

The clinician writes a RIMQL query, and it turns into SPARQL.  There's no reason you couldn't do that with HL7 FHIR either.





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--
Jerven Bolleman
me@jerven.eu<mailto:me@jerven.eu>

Received on Tuesday, 2 October 2012 18:07:49 UTC