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(unknown charset) HL7 XML example - second

From: (unknown chars <ogbujic@bio.ri.ccf.org>
Date: Wed, 21 Feb 2007 09:30:16 -0500 (EST)
To: (unknown charset) public-grddl-wg <publi
Message-ID: <Pine.GSO.4.60.0702210922330.23749@joplin.bio.ri.ccf.org>
So, I finally got the chunk of time to do the HL7 primer usecase justice. 
I suffered some data loss on my latop and had to redo alot of earlier 
work.  No worries, I got several things done which I wanted to address to 
finish this off:

- Move the documentation of the medical record target ontology off ESW to a permanent namespace document
- A namespace document which has as  GRDDL result the OWL ontology itself
- Better references to literature and supporting ontologies
- Compliance with the community of Ontology of Biomedical Ontologies (OBO) [1] as well as DOLCE [2]
- Go through a second review of the target ontology (added annotations, ..)
- Flesh out the GRDDL transform to cover as much of the input HL7 document as possible

The human/machine readable documentation of the medical record ontology is 
available from the namespace URL

   http://purl.org/cpr/0.5#

This only documents the cpr:* terms and a handful of dependent terms.  The 
*full* documentation is available from

   http://purl.org/cpr/html/full

So, we can either host the ontology (also attached) in the primer webspace 
or just point to the permanent PURL.

The attached snippets were generated by *running* the instance through a 
4Suite / RDFLib pipeline (via Bash and pipes) so it would be a shock if 
they weren't both well-formed and reproducable by any other XML-compliant 
processor.

References to SNOMED-CT are hard to come by as it is a proprietary (but 
widely used) clinical terminology.  At best their web site (linked from 
the current draft) is the most consistent URL.  Hopefully, this changes 
some day soon =)

Attached:

   - hl7-sample.xml        The source HL7 CDA [4] sample document
   - hl7-sample.rdf        RDF/XML GRDDL result
   - hl7-sample.turtle     (human-readable) Turtle GRDDL result
   - hl7-rim-to-pomr.xslt  (The GRDDL transform itself)
   - problem-oriented-medical-record.owl (the ontology itself)

Perhaps of interest to the WG, the HTML namespace document for the 
ontology was generated with a program [4] which can do this for any other 
OWL document.  It makes for a quick and dirty way to generate highly 
accessible ontology namespace documents.

The Turtle snippets need to be changed to reflect the changes:

[ a cpr:patient-record;
          dc:date "2000-04-07";
          edns:about [ a galen:Patient;
                       foaf:family_name "Levin";
                       foaf:firstName "Henry"];
          foaf:maker [ a foaf:Person;
                       foaf:family_name "Dolin";
                       foaf:firstName "Robert"]]


[ a cpr:clinical-description;
                  cpr:description-of [ a cpr:screening-act;
                                       edns:realizes [ a cpr:medical-sign;
                                       cpr:interpretant-of [
                                          a foaf:Image;
                                          skos:prefLabel "Chest-X-ray"];
                                       skos:prefLabel "Chest hyperinflated"];
                                       skos:prefLabel "Imaging interpretation"]],


[ a cpr:clinical-description;
                  cpr:description-of [ a cpr:therapeutic-act;
                                       dc:date "2000-04-07T14:30:00";
                                       galen:hasSpecificLocation "Left forearm";
                                       skos:prefLabel "Suture removal"]]

Namespace definitions (at the top of the namespace document for the medical record ontology):

- cpr->    http://purl.org/cpr/0.5#
- edns->   http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#
- dc->     http://purl.org/dc/elements/1.1/
- galen->  http://www.co-ode.org/ontologies/galen#

[1] http://obo.sourceforge.net/
[2] http://www.loa-cnr.it/DOLCE.html
[3] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16221939&query_hl=1
[4] http://code.google.com/p/python-dlp/wiki/SemanticWebOntologyPublisher

Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593
ogbujic@ccf.org

Received on Wednesday, 21 February 2007 14:30:27 GMT

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