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

From: <DAN.RUSSLER@ORACLE.COM>
Date: Fri, 25 Aug 2006 22:27:20 +0000 (GMT)
Message-ID: <28140283.1156544840803.JavaMail.oracle@web265.oracle.com>
To: helen.chen@agfa.com
Cc: public-semweb-lifesci@w3.org
Thanks Helen,
I have some questions on your notes below that I'm afraid will display my ignorance and naivete in RDF. In addition, I don't have access to Protege and some of my questions may be well-answered there.
As you discussed classCodes and inheritance below, I didn't catch how moodCode was included.
In HL7, because an instance (read "resource) of classCode is always required to be associated with a moodCode, and because neither classCode nor moodCode can be changed once an instance is created, it seems natural to always express ontology relationships with a concatenation of classCode and moodCode. Therefore, to map inheritance in UML to "class" in RDF, it seems natural to create all the attributes associated with the HL7 classCode and its super classes as properties in the RDF class expressions for each concatenated HL7 classCode-moodCode.
Is this what you were saying below?
Also, as I understand from W3C documents, an association class in UML always maps to a predicate in an RDF triplet. So the HL7 typeCodes in ActRelationship, Participation, and RoleRelationship would all map to the predicate in the RDF triple that joins two classCode-MoodCode Subject/Objects in RDF.
Is this also what you were saying below?
Sorry for these questions if the answers are obvious. It will help me understand better....Thanks

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

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


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
SubjectRE: 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 Saturday, 26 August 2006 03:58:00 GMT

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