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Implications and Issues in Converting UML to RDF/OWL When Constructing HL7 RIM Ontology

From: <helen.chen@agfa.com>
Date: Fri, 8 Sep 2006 17:12:37 -0400
To: DAN.RUSSLER@ORACLE.COM
Cc: public-semweb-lifesci@w3.org
Message-ID: <OF8581CA1E.9F72B4B2-ON852571D5.0064B055-852571E3.00748283@agfa.com>
Hi, Dan

Given the detailed description of HL7 RIM and Domain Vocabulary, it is 
quite tempting to generate the RIM ontology directly from some kind of 
conversion scheme between UML and RDF/OWL , preferably some automated 
tools/scripts. 

I assume you must aware some similar efforts in generating RIM ontology. 
One such ontology is made by Bhavna Orgun 
(http://www.ics.mq.edu.au/~borgun/Software.html). 

However, when examining closely the fundamental theories behind UML (OO) 
and RDF/OWL (Model theory), you will find that the direct translation from 
UML to RDF/OWL is not so straightforward as it seems.  For example:

1. Mapping UML classes to RDF classes
 UML class hierarchy is shown in class diagram.  In a typical OO fashion, 
if class B is the subClass of class A, all attributes of A will be 
"inherited" by B.  Furthermore, class B often will have additional 
attributes that impose further restrictions on B.  RIM class diagram only 
shows those subclasses that have additional attributes compare to their 
super-classes.  Translation of RIM class diagram into RDF/OWL classes and 
subclasses can be quite misleading.   I find a more adequate 
categorization is the class type list in the domain vocabulary, for 
example, for classification of the act class, I have used  the domain 
ActClass ("A code specifying the major type of Act that this act-instance 
represents" ). 

2. Mapping UML attributes RDF properties
In OO, all attributes of a class will be inherited by its subclasses.  In 
RDF/OWL, there is not such "inheritance", such that 

{?A ?P ?X. ?B rdfs:subClassOf ?A} => {?B ?P ?X} 

(the above rule does not exist in OWL semantics)

Some semantics in OO inheritance can be mapped to RDF/OWL using 
restrictions, but great care must be applied not to over-restrict your 
ontology.  Maybe we can look at some details during one of our Tcon. 

3. Mapping "relationship classes" to RDF property

There are "relationship classes" in RIM, such as ActRelationship class, 
RoleLink class.    These classes are used to state relationship between 
two acts, or two roles.  In OO, they are designed as classes, and can be 
easily mapped to the ER model for database, in order to accommodate 
one-to-many relationship.  In RDF/OWL, it is natural to model them as 
properties, and their types as sub-properties.  This is how they are 
modelled in our RIM ontology mentioned in my previous email. 

These are a few points I have encountered during my exercise of 
constructing RIM Ontology. 

I am copying HCLS list on this subject, hope to hear from other people's 
experience in "converting RIM ontology from UML" or from UML->OWL in other 
domains.  Many domain knowledge is captured in UML type of models and 
diagrams. If we can find a good way to convert these domain knowledge in 
UML to OWL, I believe it would offer some value for Informatics as 
general.

Kind regards.

Helen







http://www.agfa.com/w3c/hchen




DAN.RUSSLER@ORACLE.COM 
08/25/2006 12:34 PM

To
Helen Chen/AMPJB/AGFA@AGFA
cc

Subject
RE: invitation for next ACPP call







Thanks for the welcome Helen. I hope to learn a lot and perhaps, at least, 
contribute a little. 
I've been exploring transforms from UML to RDF and have found some 
resources. Do you have anything written on mappings or transforms from the 
RIM to RDF expressions?

Dan Russler, M.D.
VP Clinical Informatics
Oracle
(VM) 404-439-5983
--- Original Message ---




Hi, Dan and the group 

My sincere apology to all with regard to this week's ACPP Tcon.   I was on 
vacation the whole week and did plan to attend the Tcon on Tuesday.  Due 
to a health problem of my father, I ended up only getting back to my 
computer this morning. 

Welcome, Dan, to this group.  It is so good to hear your interest in 
working on HL7 RIM ontology.  We have the same intention and worked on a 
draft which you can find at ACPP group's attachments section: 

http://esw.w3.org/topic/HCLS/ACPPTaskForce?action=AttachFile 

You can download the RIMV3OWL.zip file which contains all files of RIM 
ontology in protege.    I had some design consideration and choices made 
during the design and implementation of this ontology and discussed them 
once with Chimizie.  I am very much looking forward to hearing your 
comments and working together. 

I hope to talk with all of you on our next Tcon at 3pm, Tuesday, August 
29.   

Kind regards. 

Helen 
http://www.agfa.com/w3c/hchen




"Davide Zaccagnini" <davide@landcglobal.com> 
08/22/2006 08:27 AM 


To
<DAN.RUSSLER@ORACLE.COM>, <ogbujic@bio.ri.ccf.org>, 
<thongsermeier@partners.org>, Helen Chen/AMPJB/AGFA@AGFA, 
<Alfredo.Morales@cerebra.com>, "'Brandt, Sam \(MED US\)'" 
<sam.brandt@siemens.com> 
cc

Subject
RE: invitation for next ACPP call









Dan,

Here are the details 

SW_HCLS(ACPP) 
SW Life Sciences IG 
Tuesdays 
3:00pm-4:15pm
+1.617.761.6200, conference code 2277 ("ACPP")

Regards

Davide

-----Original Message-----
From: DAN.RUSSLER@ORACLE.COM [mailto:DAN.RUSSLER@ORACLE.COM] 
Sent: Monday, August 21, 2006 6:18 PM
To: ogbujic@bio.ri.ccf.org; thongsermeier@partners.org; 
helen.chen@agfa.com;
Alfredo.Morales@cerebra.com; davide@landcglobal.com; Brandt, Sam (MED US)
Subject: Re: invitation for next ACPP call

Thanks!...I'm looking forward to working with this group.

Can someone send call-in information?


Dan Russler, M.D.
VP Clinical Informatics
Oracle
(VM) 404-439-5983

--- Original Message ---
> 
> I second that!
> Welcome Dan!!
> 
> -Sam
> 
> 
> -----Original Message-----
> From: Hongsermeier, Tonya M.,M.D. <THONGSERMEIER@PARTNERS.ORG>
> To: Davide Zaccagnini <davide@landcglobal.com>; helen.chen@agfa.com
> <helen.chen@agfa.com>; DAN.RUSSLER@ORACLE.COM <DAN.RUSSLER@ORACLE.COM>;
> Chimezie Ogbuji <ogbujic@bio.ri.ccf.org>; Alfredo Morales
> <Alfredo.Morales@cerebra.com>; Brandt, Sam (MED US)
> Sent: Mon Aug 21 17:54:34 2006
> Subject: RE: invitation for next ACPP call
> 
> Davide
> 
> This is fantastic, Dan, welcome to the team
> 
> Best
> 
> Tonya
> 
> 
> 
> Tonya Hongsermeier, MD, MBA 
> Corporate Manager, 
> Clinical Knowledge Management and Decision Support 
> 
> Partners HealthCare System 
> Clinical Informatics Research and Development 
> 93 Worcester Street, PO Box 81905 
> Wellesley, MA 02481 
> P: 781.416.9219     Mobile: 617.717.8711 
> Fax: 781.416.8912 
> 
> ________________________________
> 
> From: Davide Zaccagnini [mailto:davide@landcglobal.com] 
> Sent: Friday, August 18, 2006 3:00 PM
> To: helen.chen@agfa.com; DAN.RUSSLER@ORACLE.COM; Hongsermeier,
> Tonya M.,M.D.; Chimezie Ogbuji; Alfredo Morales; sam.brandt@siemens.com
> Subject: invitation for next ACPP call
> 
> 
> 
> Hi All,
> 
> 
> 
> I would like to invite to our next ACPP call Dan Russler, VP
> of clinical informatics at Oracle. Dan is interested in
> approaches to map HL7 RIM to RDF and in modeling clinical
> protocols with semantic technologies. 
> 
> 
> 
> Dan, 
> 
> here is the link to our wiki page where we can start looking
> at the work we have done so far
http://esw.w3.org/topic/HCLS/ACPPTaskForce#preview
> 
> 
> 
> Are we ok for next Tuesday at 3pm?
> 
> 
> 
> Regards
> 
> 
> 
> Davide 
> 
> 
> 
> 
> 
> 
> 
> Davide Zaccagnini, MD, MS
> 
> Product Manager, Medical Informatician
> 
> + 1 617 864 1031 (Office)
> 
> + 1 617 642 7472 (Cell)
> 
> davide@landcglobal.com
> 
> www.landcglobal.com
> 
> 
> 
> 
>
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Received on Friday, 25 August 2006 23:02:51 GMT

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