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

From: William Bug <William.Bug@DrexelMed.edu>
Date: Sun, 27 Aug 2006 14:17:56 -0400
Message-Id: <FAC432DE-E368-46EF-AD33-08938315BDB6@DrexelMed.edu>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, helen.chen@agfa.com, public-semweb-lifesci@w3.org
To: DAN.RUSSLER@ORACLE.COM
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&dopt=AbstractPlus&list_uids=16387553&query_hl=2&i 
tool=pubmed_docsum
		http://www.sciencedirect.com/science? 
_ob=ArticleURL&_udi=B6WHD-4HRN3GB-1&_coverDate=06%2F30% 
2F2006&_alid=439843079&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6848&_sort= 
d&view=c&_acct=C000007158&_version=1&_urlVersion=0&_userid=95578&md5=8be 
fcae03811ddf4a1101c027f020dc5
		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-z 
SkzS&md5=bcd20c1e022879d25c7d5f70e4cc4707&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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> > Thank you
>
>
>
> >
>
>

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)


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Received on Sunday, 27 August 2006 18:18:31 GMT

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