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

Hi All,
 
There is there Ontology Definition Metamodal specification that is an
soon to be adopted specification from the OMG that was put together by
IBM and Sandpiper (http://www.omg.org/docs/ad/06-05-01.pdf) that
provides quite a bit of insight into the relationship between UML and
OWL and provides mappings at different levels between the two.
 
cheers,
Michael
 
Michael Miller 
Lead Software Developer 
Rosetta Biosoftware Business Unit 
www.rosettabio.com 

	-----Original Message-----
	From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of William Bug
	Sent: Sunday, August 27, 2006 11:18 AM
	To: DAN.RUSSLER@ORACLE.COM
	Cc: Kashyap, Vipul; helen.chen@agfa.com;
public-semweb-lifesci@w3.org
	Subject: Re: Implications and Issues in Converting UML to
RDF/OWL When Constructing HL7 RIM Ontology
	
	
	Hi Dan, 
	
	
	This a very helpful foundation to start from, Dan.  I would
suggest selecting 4 - 5 very specific examples of this use case,
preferably covering across the examples of family medical history
clinical statements including a variety of different semantic entities -
e.g., genetic information, documented treatments of relatives for
disorders that include a genetic component, environmental conditions
including life style info and socio-economic status, etc..  Would it be
possible to build on the stroke victim Use Case Helen et al. have
assembled on the Wiki
(http://esw.w3.org/topic/HclsigDscussionTopics/HclsSubGroupACPP)?
	
	
	I would also give an strong endorsement of of Vipul's statement
"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."
	
	
	One thing is for certain, "definitely require" should be
substituted for "probably need" in the quote above.
	
	
	
	I would also add the following: 
	
	
	A) UML is an immensely useful formalism for creating or
communicating to others a given computable information model.
Unfortunately, despite the many similarities between the process by
which a formal OOP class-based model designed to compute on real-world
artifacts and the process by which one constructs an formal ontological
framework to characterize real-world entities, these two orientations
toward creating practical, computational infrastructures have many
conflicting requirements.  
	B) As an example, the specific nature of UML-style modeling
created to support OOP system development and - in some circumstances -
interoperability (between implementation languages and persistence
mechanisms, for instance) tend to have properties that are orthogonal to
the goals of ontology development and ontology application.  This is
even true when one considers the mechanisms provided in UML and/or XML
for extending and combining models.
	C) The general issue when it comes to developing semantically
mediated systems interoperability (such as would be required for the Use
Case you describe here, Dan) is the dual goal of designing a mechanism
and consequently implementing an infrastructure both widely applicable
to the problem domain AND effective to the required level of semantic
granularity on any specific example case can also often conflict with
one another.  The only way to be certain the technical solution you
propose "has legs" is to work through SEVERAL QUALITATIVELY DISTINCT
examples of the Use Cases driving the creation of the system.  This is
even more true for semantically oriented computational infrastructures
than it is for those built around a fixed information model. 

	For a helpful overview of how these issues hold for HL7 RIM, I'd
recommend reviewing the following:
	1) HL7 RIM: An Incoherent Standard, Smith, B and Ceusters, W.
(August 2006)
	http://ontology.buffalo.edu/HL7/doublestandards.pdf

	2) Methods in biomedical ontology., Yu, A.C. (2006), J Biomed
Inform. 2006 Jun;39(3):252-66
	
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dop
t=AbstractPlus&list_uids=16387553&query_hl=2&itool=pubmed_docsum
	
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WHD-4HRN3GB-1
&_coverDate=06%2F30%2F2006&_alid=439843079&_rdoc=1&_fmt=&_orig=search&_q
d=1&_cdi=6848&_sort=d&view=c&_acct=C000007158&_version=1&_urlVersion=0&_
userid=95578&md5=8befcae03811ddf4a1101c027f020dc5
	
http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WHD-4HRN3GB-1-
W&_cdi=6848&_user=95578&_orig=search&_coverDate=06%2F30%2F2006&_qd=1&_sk
=999609996&view=c&_alid=439843079&_rdoc=1&wchp=dGLbVzz-zSkzS&md5=bcd20c1
e022879d25c7d5f70e4cc4707&ie=/sdarticle.pdf

	The former is a well-informed review of the conflicting HL7 RIM
objectives of providing BOTH an information model AND a reference
ontology.  It's a bit stern in tone, but it's purpose is very much
constructive in nature.  I'm not an expert in the use of HL7-RIM, so I'd
most definitely defer to others on this list to provide counter
arguments to the issues they raise most specifically as relates to 'B'
and 'C' above.  The basic recommendation is to simply separate the
data/info modeling from the reference ontology features into two
distinct efforts, analogous to the way FuGE and FuGO approach this issue
for functional genomics information.

	The later is an excellent overview providing a clear sense of
how and why to avoid conflating data modeling with ontological
engineering.  It only very briefly touches on HL7-RIM, but the entirety
of the review is extremely relevant to this topic.

	I don't mean to appear overly didactic here.  Quite the opposite
- working with folks on this list has been an immensely valuable
learning experience for me.  I just thought it would be helpful to
provide a brief overview of the specifics on this issue Vipul has raised
in the context of HL7-RIM.

	Cheers,
	Bill
	
	

	On Aug 27, 2006, at 11:11 AM, DAN.RUSSLER@ORACLE.COM wrote:


		Hi Vipul,

		Excellent comments...It seems to me that an ontology
that doesn't have a testable use case can never be judged useful or not
useful for any kind of predictable search strategy.

		Here is the use case I would like to explore:

		"An RDF system has been put in place to navigate to
healthcare resources stored in many systems including genetic resources,
proteomic resources, and healthcare medical record resources. One of the
healthcare resources is a CDA document, which itself has a URI. However,
within the CDA document, are detailed resources expressed as HL7 RIM
Acts which also carry URI's. I would like to navigate from my RDF-based
navigation system to a specific kind of HL7 RIM Act, e.g. a family
medical history clinical statement, within a specific kind of CDA
document. "

		I'm sure this use case could be better written with a
little time. However, is this the kind of use case you were looking for?
		
		Dan Russler, M.D.
		VP Clinical Informatics
		Oracle
		(VM) 404-439-5983
		--- Original Message ---
		

		> 
		
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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> 


	
	Bill Bug
	Senior Research Analyst/Ontological Engineer

	Laboratory for Bioimaging  & Anatomical Informatics
	www.neuroterrain.org
	Department of Neurobiology & Anatomy
	Drexel University College of Medicine
	2900 Queen Lane
	Philadelphia, PA    19129
	215 991 8430 (ph)
	610 457 0443 (mobile)
	215 843 9367 (fax)


	Please Note: I now have a new email - William.Bug@DrexelMed.edu




	
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