Re: [TMO] coding XML patient data in the Indivo schema

A few suggestions on transforming XML patient records to RDF:

1. Gloze, which does bidirectional XML<->RDF mapping:
http://jena.hpl.hp.com/juc2006/proceedings/battle/paper.pdf 
Hmm, it looks as though that link may be broken.  :(
But the paper also seems to be cached here:
http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=7119E436200DD4FBA3914AFC5824A4C4?doi=10.1.1.88.8929&rep=rep1&type=pdf 
And the code is on sourceforge:
http://jena.sourceforge.net/contrib/contributions.html

2. I favor doing all significant transformations at the RDF level -- not
XML.  In other words, transform to/from XML only at the edges, using a
trivial transformation between XML and RDF, and then use ontologies and
rules to transform to/from that RDF and RDF that is expressed in your
preferred ontology, as illustrated on slide 21 of "RDF as a Lingua
Franca: Architectural Strategies":
http://dbooth.org/2009/stc/dbooth-SemTechConf-2009.ppt

3. I suggest avoiding custom XML transformations.  I think it's
generally better to use standard XML transformations (such as by using
Gloze) and push the work to the RDF level, as mentioned above, because:
(a) XML has more tedious syntactic details; and (b) you are using
ontologies and rules anyway for other things, so it makes the system as
a whole simpler and easier to maintain if don't also need to maintain a
set of XSLT transformations.

4. I see some Indivo namespace URIs such as these being used:
http://indivo.org/vocab/xml/documents
http://indivo.org/codes/ndc
http://indivo.org/codes/units
But all of them seem to be 404, so I cannot easily figure out what they
are intended to mean.  :(   If anyone knows who is responsible for
maintaining these URIs, please ask them to un-break them or turn them
into PURLS (see http://purl.org/ ), following the URI guidelines in 
http://www.w3.org/TR/cooluris/  ,
so that they can be dereferenced to useful information, rather than
forcing everyone to needlessly search the web and guess what they are
supposed to mean.

thanks,
David

On Sun, 2010-07-18 at 22:56 -0400, Eric Prud'hommeaux wrote:
> Thomas Gambet and I have been transforming the XML patients (ordinary
> citizens like you and me, tragically afflicted with XML) to follow the
> Indivo schema. Indivo uses a bunch of small schemas to represent
> e.g. contacts and problems, so we've put together an envelope schema
> which references the Indivo schema for most of its meaty data. We
> still have some coding to go, but folks can go take a look at
>  data:
>   http://dvcs.w3.org/hg/TMO-Indivo/file/tip/syntheticPatients/AD_PCHR_1-indivo.xml
>  schema:
>   http://dvcs.w3.org/hg/TMO-Indivo/file/tip/syntheticPatients/indivo-schemas/envelope.xsd
> 
> Places where the envelope schema reference other schmeme types, e.g.
>   <xs:complexType name="PrescriptionsType">
>    <xs:sequence>
>     <xs:element name="Prescription" type="indivo:Prescription" minOccurs="0" maxOccurs="unbounded"/>
>    </xs:sequence>
>   </xs:complexType>
> , have been mapped to Indivo. Places where we have lots of elements
> defined didn't have a pre-existing Indivo schema. Lots of thanks to
> Thomas for working on this stuff.
> 
> Folks in the HCLS IG have commit privileges on this Mercurial
> repository. Once we finish coding the patient encounters, we'll get
> serious about mapping out the patient RDF ontology. The XSLT we use
> for this will also be useful for mapping anyone's Indivo data to RDF.
> 
> Thoughts? Suggestions?


-- 
David Booth, Ph.D.
Cleveland Clinic (contractor)
http://dbooth.org/

Opinions expressed herein are those of the author and do not necessarily
reflect those of Cleveland Clinic.

Received on Wednesday, 21 July 2010 19:14:20 UTC