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

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Sun, 27 Aug 2006 08:22:15 -0400
Message-ID: <2BF18EC866AF0448816CDB62ADF6538104C16057@PHSXMB11.partners.org>
To: <helen.chen@agfa.com>, <DAN.RUSSLER@ORACLE.COM>
Cc: <public-semweb-lifesci@w3.org>
I agree with Helen. In general, we need to be very careful about translating
from the UML to the OWL meta-model.

It is quite likely that there are multiple alternatives in OWL for representing
the same UML construct and we would

probably need best practices for the same.

 

Towards this end, it would be very useful to understand the use cases and
requirements for which this translation is required.

The questions we need to answer are:

-          What is the value of this translation? May be for the particular use
case and requirement, it's not really useful?

-          What are the assumptions behind the use cases? Typically these
assumptions would help determine a more appropriate 

and accurate translation.

 

RIM appears to be more of a "meta-model" rather than an "ontology" and the
semantics of the various constructs have not been

defined accurately. There has been a lot of discussion. Also, one needs to
understand issues related to whether we are building an information model

for HL7 message content or an information model for persistence to be mapped
into a database schema or one for decision support?

 

I would strongly recommend that this exercise, which is very valuable, should be
carried out in the context of a well defined use

case. Doing it in the abstract could result in making arbitrary modeling
decisions which may detract from the usefulness of the

translation.

 

Cheers,

 

---Vipul

 

________________________________

From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of helen.chen@agfa.com
Sent: Friday, September 08, 2006 5:13 PM
To: DAN.RUSSLER@ORACLE.COM
Cc: public-semweb-lifesci@w3.org
Subject: Implications and Issues in Converting UML to RDF/OWL When Constructing
HL7 RIM Ontology 

 


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 Sunday, 27 August 2006 12:22:35 GMT

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