Hi, This is an interesting discussion. I think we need to keep a sense of purpose here in what we are doing. We need to understand that the complexity of biomedicine is probably unsurpassed and the language of health professionals is a way of dealing with this. It has historical roots which allows people to drill down when appropriate. The paper by Werner and Barry on malaria illustrates the difficulties. So we will find, if we look hard enough, that there are massive imperfections in what clinicians record but these imperfections are generally understood by those that need to know about them.
I remember a story about a medical teacher when I was young asking a rather impertinent student what they knew about the cause of rheumatoid arthritis. He said "Nothing". And then he asked the student "And what do I know about the cause?" He again said "Nothing". The teacher nodded and added "But don't underestimate the gap between what you know about the cause of rheumatoid arthritis and what I know". We don't call rheumatoid arthritis idiopathic arthritis because we have accepted the syndrome and its histological features. We know the prognosis and outcomes in many situations. Patient's would like to know why - but we can't tell them. Malaria is actually four diseases - two of which actually are rather different from the other two. Pneumonia, from the perspective of causation, is actually 100s of diseases all with a similar pathology. When I read the paper on malaria by the ontology guys I learned a lot. I have diagnosed and treated malaria quite a few times in my life but did not know some features of the life cycle of the plasmodium and the features that Werner and Barry are describing at times are not of clinical significance. So where does ontology get in the way of good health care? I would suggest it is when there is no 'drill down'; that complexity is presented as a flat knowledge space. Deep knowledge in clinical practice, what is needed to provide the best care, is not necessarily detailed knowledge - the latter is usually the preserve of bioscientists and clinicians researching an area. They might come back to us with more detail that alters the knowledge required to provide the best care. It is then that deep knowledge shifts. More detailed knowledge does not necessary lead to more complex deep knowledge. Asthma is a good example. Treatment used to be a nightmare but as we have learned more it is really quite simple to manage. So I just want to challenge the approach of linking to ontologies. I would like to propose a simplification. If we take the archetypes as the purest expression available of what clinicians want (or are able) to record then we have something. We can organise and classify these in future to make them very available. CKM has started that process and it will get more sophisticated. The task then for term_bindings is to link points in archetypes to terminology so that other people can understand from that perspective what we are talking about. I would argue that there are two approaches. First is to find a term in a terminology that says exactly what the archetype is recording. The second approach is to find the observable entity that is being recorded. It becomes absurd at one level to think about the things that you might describe: - the notion of the thing that might be observed (blood CO2 level) - the procedure for measuring it (which might be complex) and everything about that - the recording of the value of the thing that has been observed and any confounding factors - the actual value of the thing observed. The archetype actually records many of these things as well as the value. A pure ontology for such a thing will get massively complex. Do we have the procedure for measuring the confounding factors, the recording of the procedures for measuring them, the actual value of these etc. If we are measuring the blood gas there may be may features of the measuring process that we want to record - do we have observable entities for all of these, procedures for measuring them and recording and values. I hope you can see where we are going here. We have to stay anchored in what is useful and effective clinical practice. The fractal nature of this is becoming clear and we will see just how fractal things get when we start recording genetic features of cancers (and people). I think we should start by working purely with term_bindings for the observable entity that is expressed in the archetype - as a whole and then for each entry in the data section of the observation if that is helpful. I find this a very fruitful area of enquiry and I do not want to stifle it at all - just to point out that what might appear imperfections often are important kludges that are shared widely and work in real practice. Cheers, Sam > -----Original Message----- > From: openehr-technical-bounces at chime.ucl.ac.uk [mailto:openehr- > technical-bounces at chime.ucl.ac.uk] On Behalf Of Fabrice Camous > Sent: Friday, 12 March 2010 2:47 AM > To: openEHR-technical at openehr.org > Subject: Re: Term bindings in archetypes and templates > > Thanks Stef, > > It's a nice paper indeed, and it formulates the confusions I had about > SNOMED, which is covering different perspectives of the medical > reality. > But this leads me to questions I have precisely about the bindings of > the ontology part of the archetype. They may need to be more specific. > Depending on what ontology we bind to (and here I include everything > documenting reality, a reality including models, archetypes, > everything!), the binding will have different meanings. For example, > let's say we have an archetype node at0000 which we name "blood > pressure" in an openEHR.OBSERVATION archetype and we wish to bind this > node to an external terminology. I can see three kinds of bindings: > 1) Let us assume that there is, available to us, an ontology of > information-bearer (or information container) entities, the development > of which is so advanced that there is actually a type of such > information-bearer entities which corresponds perfectly to the > recording > of a blood pressure observation, the so-called "perfect match". And by > that I'm not saying that the ontology also indicates that such a type > has whole-part relationships with recording of systolic blood pressure > observation, etc, which is another problem. Well even if this "perfect > match" exists, and since the paper introduced by Stef mentions the > realist ontological approach (OBO, BFO), I will use their distinctions > and say that the EHR is about particulars (instances) and the > information-bearer ontology about universals (types, categories, > kinds). > Therefore, the binding here is a relationship which we would call > "instance-of". Note that OBO also develops an ontology of relationships > (RO, http://www.obofoundry.org/ro/) where you can find an "instance_of" > relationship. > 2) Now let's consider that the ontology we want to bind our at0000 node > to describes observations, but not their recording. It means that the > ontology encountered in 1) was documenting the recording of > observations > (which, I think, is what an obervation archetype does). In this case we > can not use "instance-of", but something like "recording-of" if it > exists in the relation ontology. Note that technically, we should > probably bind to the particular instance of the blood pressure > observation, not directly to the type (category, universal). We may > have > to compose/coordinate relationships. Something like "recording-of" + > "instance-of". > 3) Finally let's say that we have available an ontology which is not > about the information-bearer entities, not about observations, but > about > "dependent continuants" (entities which endure, but depend on another > entity for existing) which we observe, for example qualities, such as > the blood pressure is the quality of a human, or a blood system. We > need > an "observation-of" relationship, and the final binding will look like > "recording-of" + "observation-of" + "instance-of". > > The relationships help the system to make sense of the meaning pointed > to in the archetype ontology and thus actually use the > reasoning/knowledge available externally. Is there a way to integrate > them in the AOM? > > > > > Stef Verlinden wrote: > > For those of you interested in the 'problems' within Snomed as an > ontology, here (http://precedings.nature.com/documents/3465/version/1) > you can find a good and recent article describing them. This doesn't > mean we shouldn't use Snomed, but knowing where the problems are is > helpful to find solutions as Thomas already stated. > > > > Cheers, > > > > Stef > > > > > > Op 11 mrt 2010, om 11:06 heeft Mikael Nystr?m het volgende > geschreven: > > > > > >> Hi Michael, > >> > >> I agree that post-coordination is useful when mapping to SNOMED CT > and it > >> works well in many cases. However, to be able to create post- > coordinated > >> concepts the pre-coordinated "building blocks" have to already exist > in the > >> terminology, which are not always the case. There are sometimes also > harder > >> to reuse information mapped to post-coordinated concepts than > >> post-coordinated concepts, because the hierarchies around the > >> post-coordinated concepts are generally not so tailored for the > >> post-coordinated concepts as the hierarchies around pre-coordinated > concepts > >> are. > >> > >> It is also only SNOMED CT and a few other terminology systems that > allow > >> post-coordination, so for the majority of terminology systems > >> post-coordination isn't possible to use. > >> > >> My view is therefore still that creating archetypes and the > terminology > >> bindings in parallel is better than fist create the archetypes and > >> afterwards add terminology bindings. > >> > >> Greetings, > >> Mikael > >> > >> > >> > >> -----Original Message----- > >> From: openehr-technical-bounces at chime.ucl.ac.uk > >> [mailto:openehr-technical-bounces at chime.ucl.ac.uk] On Behalf Of > >> Michael.Lawley at csiro.au > >> Sent: den 11 mars 2010 01:46 > >> To: openehr-technical at chime.ucl.ac.uk > >> Subject: Re: Term bindings in archetypes and templates > >> > >> > >> Hi Mikael, > >> > >> You may be interested in our mapping tool, Snapper, which is > designed to > >> tackle this problem for mapping to (not from) SNOMED CT. It > provides > >> extensive support for mapping to post-coordinated expressions where > >> single-concept maps are not possible and can be used to create > unofficial > >> extensions to SNOMED CT. > >> > >> More details and a short screen-cast are on our website > >> http://aehrc.com/snapper > >> > >> Cheers, > >> michael > >> > >> -- > >> Dr Michael Lawley > >> Principal Research Scientist > >> The Australia e-Health Research Centre http://aehrc.com/ > >> +61 7 3253 3609; 0432 832 067 > >> > >> "Ein Fl?gel und einen Schnabel machen kein Vogel" > >> > >> > >> On 11/03/10 9:49 AM, "Mikael Nystr?m" <mikael.nystrom at liu.se> wrote: > >> > >> Thomas Beale wrote: > >> > >> > >>> On 10/03/2010 22:16, Mikael Nystr?m wrote: > >>> > >>>> I belong to a group that, except for openEHR related research, > also do > >>>> research about terminology systems and terminology systems > mapping. > >>>> During mapping from one terminology system to another terminology > >>>> system is it quite common to be unable to map properly, because > the two > >>>> terminology systems have divided the domain in different ways. > This > >>>> problem appears even when mapping to SNOMED CT, which have a broad > >>>> coverage and a concept model allowing a broad set of > relationships. My > >>>> view is that the same problem will appear when finalized > archetypes are > >>>> bound to existing terminology systems. > >>>> > >>> it will certainly appear. The question is: for those archetype > nodes that > >>> it is useful to bind to terminology (likely to be 10% or less), how > close > >>> is the match? For example, in labs, it should be nearly spot on. > For > >>> anatomy, it should be pretty close. For diseases, the disease > concept in > >>> an archetype will assume that it is coded in the first place by > >>> terminology, so the only problem there is mapping problems from ICD > to SCT > >>> etc. I think we need to look at the actual size of the concrete > problem, > >>> not its theoretical worst case. > >>> > >> I agree that we have to wait and see how much problems we will get. > That was > >> also my reason to reply to Sebastian's e-mail which told that there > is no > >> problem to add terminology bindings after the archetypes are > finalized. > >> > >> However, I didn't refer to "theoretical worst case". I referred to > actual > >> problems that have appeared for us during both our research work and > in our > >> national SNOMED CT project in Sweden. > >> > >> Greetings, > >> Mikael > >> > >> > >> _______________________________________________ > >> openEHR-technical mailing list > >> openEHR-technical at openehr.org > >> http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-technical > >> > >> > >> _______________________________________________ > >> openEHR-technical mailing list > >> openEHR-technical at openehr.org > >> http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-technical > >> > >> > >> _______________________________________________ > >> openEHR-technical mailing list > >> openEHR-technical at openehr.org > >> http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-technical > >> > > > > > > _______________________________________________ > > openEHR-technical mailing list > > openEHR-technical at openehr.org > > http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-technical > > > > > This message has been scanned for content and viruses by the DIT > Information Services E-Mail Scanning Service, and is believed to be > clean. http://www.dit.ie > _______________________________________________ > openEHR-technical mailing list > openEHR-technical at openehr.org > http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-technical
