RE: Wait a sec...What about the HL7 RIM An Universal Exchange Language

hi peter,



"You don't gain anything by decomposing it and recomposing it into RDF."



the scenarios where i have seen this work is where the data itself isn't
touched, the application makes the transformation to RDF in memory then
applies semantic tools.  so if i want to see if there are patients suitable
for a clinical trial, a sparql query might describe the criteria quite
nicely.  then i could run over EHR records, translating to RDF triples in
memory then applying the query.



depending on the backing store, i've also seen this done successfully by
translating the query to sql then turning the query result into rdf triples
to answer the SPARQL query.



cheers,

michael



*From:* Peter.Hendler@kp.org [mailto:Peter.Hendler@kp.org]
*Sent:* Thursday, December 16, 2010 4:37 PM
*To:* mscottmarshall@gmail.com
*Cc:* conor-dowling@caregraf.com; mmiller@systemsbiology.org;
public-semweb-lifesci@w3.org; public-semweb-lifesci-request@w3.org;
twclark@nmr.mgh.harvard.edu
*Subject:* Re: Wait a sec...What about the HL7 RIM An Universal Exchange
Language



Just want to be clear about when we use the word HL7.  In the USA when you
just say HL7 it is assumed you mean Version 2 which is in very wide use and
is not OO at all.  You almost have to say RIM based or V3 before people
assume you mean the OO model (RIM).

There is a specific XML serialization of the V3 RIM called the XML ITS.  It
generates the XML elements, attributes and the order that they must be
serialized in. When you are dealing with a CDA document, then in addition to
these rules there are "templates" that are mostly just verbal human readable
rules that you must follow for a given template.  Templates refer to each
other, so the C32 document mentioned in the Meaningful Use rules of the
HITECH part of the ARRA act is made from HL7 and IHE and HITSP templates all
referring to each other.  These templates specify many things including
which vocabularies must be used (SNOMED for example for coding the
diagnosis).

For a C32 templated CDA you have no wiggle room. The XML is defined.  You
don't gain anything by decomposing it and recomposing it into RDF.
There is nothing to say that you couldn't come up with different ITS's  For
example you could come up with a JSON ITS and I suppose you could also come
up with another RDF ITS. I'm just not convinced it would add anything to the
understandability and I think it would add a heck of a lot of size to the
representation.

 Because the diagnosis and much of the clinical data contained in a CDA is
in SNOMED, I do see the benefits of using subsumption on the SNOMED codes.
 For example you could ask for all the patients that had any form a diabetes
or heart disease and then use subsumption to get the lists of possible
SNOMED codes that would be in the records of the target patients.  What I
don't see is the advantage of using RDF instead of the standard RIM XML
syntax.

You could come up with an entirely new model for healthcare not based on the
RIM and based on RDF, but much of the world (outside the USA) is already
using the RIM.






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*"M. Scott Marshall" <mscottmarshall@gmail.com>*

12/16/2010 03:47 PM

To

conor dowling <conor-dowling@caregraf.com>

cc

Michael Miller <mmiller@systemsbiology.org>, Peter
Hendler/CA/KAIPERM@KAIPERM, twclark@nmr.mgh.harvard.edu,
public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org

Subject

Re: Wait a sec...What about the HL7 RIM An Universal Exchange Language






I like Eric Neumann's description of RDF as "recombinant data".

Agreed. Choosing something other than HL7 as the lingua franca for
assertions doesn't devalue HL7! We can be happy that we got the information
from one machine to another! It's a long haul from the days of big-endian,
little-endian. The value is not in the messages (or message syntax) but what
is in them (the cargo, the payload). But how will we interoperate between
HL7 and CDISC? I suppose that an ontology will help.. BRIDG anyone ;) Cecil?


The way that XML quietly infiltrated all our computer systems was by making
it easy to describe and parse data of all shapes and sizes. Will OWL/RDF do
the same by making it reasonably easy to describe the meaning of messages
and documents?

HL7 isn't going away. It is the standard. So, how can its users take
advantage of other (non-HL7) sources of information that are related to the
contents of its messages? And how can other systems, for example, clinical
research systems relate their information and constraints to HL7 data? See
http://hcls.deri.org/coi/demo/ (makes use of pseudo-CDISC and HL7, and Drug
Ontology), presented at AMIA. There should be machine-readable and
reason-able links from one set of assertions to the other, that can make use
of context (read: provenance). Could the HL7 provenance help us make use of
the 'cargo' in another context? i.e. assertion came from message issued
by..

-Scott

-- 
M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
Leiden University Medical Center / University of Amsterdam*
*http://staff.science.uva.nl/~marshall

On Thu, Dec 16, 2010 at 11:06 PM, conor dowling <conor-dowling@caregraf.com>
wrote:


On Wed, Dec 15, 2010 at 8:47 AM, Michael Miller <mmiller@systemsbiology.org>
wrote:
hi all,



"unambiguous identifier for "things""



i agree, this has been a known issue for many years (as you well know, tim)
but its importance is just now growing as multi-omics studies and sharing of
EHR records is becoming more common.



"It is HL7 V3"



i also agree, in a sense, with this.  HL7 messages capture information as a
whole, as an entity, so in that representation it is also true that semantic
web technologies would have a hard time, as is, making sense of them because
semantic web technologies wants a fact by fact representation, e.g. triple
store.


But turn this on its head. HL7 messages come from "islands of data" which
have undetermined linkage. Think of a lab result that has a local code,
rather than LOINC. LOINC is equivalent to a link to the outside. Effectively
the local code is meaningless outside.

By its nature, linked data should resolve. If there is a url, you should be
able to chase it down. The equivalent of a local code is a resolvable URL
which presumably leads to some sort of description of what that local
concept means, perhaps enough to translate it to a more commonly understood
equivalent.

You ask for any number of triples from a semantic endpoint, enough to
capture what you need - all lab result assertions over a period for
such-and-such a person. That's no different than a query in HL7 (or any
other RPC like mechanism).

The key difference with linked data (specifically) and "islands with
protocol access" is linkage: the idea that links always resolve to something
meaningful as opposed to identifiers that while unambiguous, may lead you no
where. The problem with the old school which Parsa's "30 years of XML and
HL7 experience" captures nicely is wrapped up in this.

I've coded this stuff a good bit and everyone gets fixated on the syntax of
messages/xml blocks. People are happy if a coded element is "correct", that
it "conforms" as opposed to being useful or meaningful. And the problem lies
not with them, but the mechanism. It's put the focus on "truck", not
"cargo".

Conor



cheers,

michael





*From:* public-semweb-lifesci-request@w3.org [mailto:
public-semweb-lifesci-request@w3.org] *On Behalf Of *Peter.Hendler@kp.org*
Sent:* Wednesday, December 15, 2010 8:18 AM*
To:* markw@illuminae.com*
Cc:* public-semweb-lifesci@w3.org; public-semweb-lifesci-request@w3.org;
twclark@nmr.mgh.harvard.edu

*
Subject:* Wait a sec...What about the HL7 RIM An Universal Exchange Language




The PCAST did not take into consideration (maybe they don't even know) there
is an universal exchange language for healthcare.  It is HL7 V3.  The CDA is
merely one of virtually infinite structures that can be constructed from the
RIM.  The meta information as well as the clinical data is unambiguously
represented by RIM.  There is no reason to ignore the thousands of man years
that went into designing the RIM.  The RIM Based Application Architecture
 (RIMBAA) work group at HL7 has had many demonstrations of RIM based
applications.  We don't need to re invent the wheel.  CDA is only one
particular RIM structure designed for one particular use case.  Those of us
who have been working at HL7 for years are blown away by the suggestion that
there needs to be a different wheel invented.

*
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*Mark <**markw@illuminae.com* <markw@illuminae.com>*>*
Sent by: public-semweb-lifesci-request@w3.org

12/14/2010 06:44 PM



To

"Tim Clark" <twclark@nmr.mgh.harvard.edu>

cc

public-semweb-lifesci@w3.org

Subject

Re: An Universal Exchange Language








But seriously, Tim, if we were to pursue this problem, we would need some
form of unambiguous identifier for "things"... and given the distributed
nature of the biomedical domain, we'd want to make sure that there was
some way of resolving that identifier to obtain metadata about it from a
variety of disparate sources who might have very different information -
clinical, molecular, demographic, etc...

hmmmm....