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Re: An HL7 RIM navigation language based on SPARQL?

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Tue, 2 Oct 2012 14:13:30 -0400
Message-ID: <CALcEXf6qzrzzy+sLzRo7kO8aQW81ArWQM09isx7Z9M=veVyPvg@mail.gmail.com>
To: Peter.Hendler@kp.org
Cc: me@jerven.eu, 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, ratnesh.sahay@deri.org
On Tue, Oct 2, 2012 at 1:54 PM, <Peter.Hendler@kp.org> wrote:

> 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.
>
>
there's an easy way to address that - which is to query for and return uri
labels, provided you have the label annotations

:someuri rdfs:label "default label" .
:someuri skos:prefLabel "a preferred community label" .
:someuri skos:altLabel "another preferred community label" .
:someuri :mypreferredlabel "my community preferred label" .

m.


> 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.
>
>
>
>
>
>
>
>
>
> *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.
>
>
>
>
>
>  *Jerven Bolleman <me@jerven.eu>*
>
> 10/02/2012 10:37 AM
>   To
> Peter Hendler/CA/KAIPERM@KAIPERM
> cc
> meadch@mail.nih.gov, 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: 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://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*<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*<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*<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.
>
>
>
>
>
>
>
>
> *
> 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.
>
>
>
>
>
> --
> Jerven Bolleman*
> **me@jerven.eu* <me@jerven.eu>
>
>


-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

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Received on Tuesday, 2 October 2012 18:14:19 UTC

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