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

From: Chimezie Ogbuji <ogbujic@bio.ri.ccf.org>
Date: Mon, 28 Aug 2006 09:45:46 -0400 (EDT)
To: w3c semweb hcls <public-semweb-lifesci@w3.org>
cc: DAN.RUSSLER@oracle.com
Message-ID: <Pine.GSO.4.60.0608280904360.27986@joplin.bio.ri.ccf.org>

On Sun, 27 Aug 2006, William Bug wrote:

> 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

This paper in particular does well to underline the issues I ran into with 
using HL7 RIM as a reference ontology and comes to the same conclusions I 
did: As a messaging standard, HL7 RIM isn't expressive or 
comprehensive enough for use as a basis for a Computer-based Patient 
Record for Clinical Research.

The conclusion that what is needed is a seperate 'Reference Ontology of
the Healthcare Domain' and a 'Model of Healthcare Information' is well 
founded.  The problem isn't so much the modelling language used for HL7 
(UML) but the intention of the standard.

HL7 is a universal healthcare messaging standard and as such is good at what it 
does.  But with regards to the Institute of Medicine's guidelines [1] for a CPR it fails to meet 
the following requirements:

- It is not sufficient for capturing complete (expressive), accurate, and longitudinal patient data
- It doesn't have any aspects of a Problem-oriented Medical Record [2] (in which the organization of Clinical information is critical for decision support)
- Its set of data elements don't have as comprehensive a coverage as the more 'formal' healthcare and life science ontogies do (such as SNOMED, UMLS, FMA, etc..) - It's semantics are ambigous (as the above paper points out)

It's best suited as a messaging interlingua between systems than as a 
primary representation model.

However, I would take the argument a step further and suggest that what is 
needed is first a common (domain-independent) framework for a CPR 
(expressed jointly in OWL and with a uniform, accompanying XML syntax) which 
captures all the aspects of longitudinal, problem-oriented patient data 
that are common across  various domains.

At the very least, the representation requirements needed for conducting effective research 
should be accomodated *first* if not the other aspects of a CPR needed for 
operational needs (such as billing, appointment booking, etc..). The 
Institute of Medicine's guidelines to this effect are well laid out.

Second, reference ontologies of specific healthcare domains should 
build on this common framework (there are already many such models that 
capture a specific domain but - as with HL7 RIM - do not by themselves 
accomodate the requirments for a CPR).

Third a model of Healthcare Information should complement this infrastructure to tackle the 
requirements specific to exchange of healthcare information between CPR systems.

[1] http://www.amazon.com/gp/product/0309055326/102-9019363-1935305?v=glance&n=283155
[2] http://www.phcsg.org/main/pastconf/camb96/mikey.htm

Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593
ogbujic@ccf.org


>
> 	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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>> 
>> 
>> 
>> >
>> 
>> 
>
> 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
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>
>
> Please Note: I now have a new email - William.Bug@DrexelMed.edu
>
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Received on Monday, 28 August 2006 13:46:07 GMT

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