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

hi david,

> 1. Gloze, which does bidirectional XML<->RDF mapping:

looks pretty straight-forward and useful.  one comment, tho, certain XML 
formulations have semantics encoded beyond the XML semantics, in 
particularly if the XML represents OWL or RDF there are links between 
elements based on attribute values that gloze would not capture.  this is 
also true of MAGE-ML and FuGE-ML (where a *_ref element refers back to the * 
element with the same identifier attribute value).

don't know how easy it would be to do but gloze might be able to read in 
from a property file rules about how elements refer back to other elements.

cheers,
michael

Michael Miller
mdmiller53@comcast.net

----- Original Message ----- 
From: "David Booth" <david@dbooth.org>
To: "Eric Prud'hommeaux" <eric@w3.org>
Cc: <public-semweb-lifesci@w3.org>; "Ben Adida" <ben@adida.net>; "Zabak, 
Steve" <Steve.Zabak@childrens.harvard.edu>; "Thomas Gambet" 
<tgambet@w3.org>; "Michel_Dumontier" <Michel_Dumontier@carleton.ca>
Sent: Wednesday, July 21, 2010 12:13 PM
Subject: 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 20:27:00 UTC