Re: Term bindings in archetypes and templates

[Thomas Beale <thomas.beale@oceaninformatics.com>]

On 01/04/2010 20:04, Fabrice Camous wrote:

Hi all,

....If we 
pretend that the reference model describes paper-based components, where 
our objects are folders, separators, sheets, it means that our 
archetypes lead to very structured pages (ignoring the folder and 
separator arrangements), with sub-sub-sections and sub-sub-paragraphs 
with sentences (leaf nodes) which are very short.

this is an interesting point. In fact what appears to happen in the reference model and archetypes taken together is that there are 3 layers of structure:

• documentary structures, i.e. Composition / Section / Entry - mainly defined by the reference model, plus archetypes for Section, and also some archetypes for things like diagnosis (a kind of Evaluation)
• real examination / observation / action techniques: archetypes whose structure directly reflects the order of examination of the body, or of performing some kind of lab work such as culturing and microscopy for microbiology result
  
• realist structures, i.e. information recorded in structures that reflects say anatomy or other real arrangements of things

An example of archetype(s) that could cover all three levels is an endoscopy report (Koray Atalag might want to add some details / URLs here). At the outer level, we have some kind of report, sections etc, then we have a structure reflecting the order of the gastroscope traversing the colon, and finally, each local observation is a collection of attributes derived from anatomy (of lumps, lesions, general characteristics like lumen etc).

Now, I suspect (I have done no study on this!) that what we really have is _only_ realist structures, but arranged firstly in an order corresponding to the order / style of examination (e.g. a systems-approach would create a different ordering of fine-grained information from a regional approach, but the fine-grained info would still be the same); all this is packaged up into documentary structures.

The lower level information should directly link to BFO structures; the next 2 levels probably don't unless BFO starts describing _kinds_ or _ways_ of examining a patient, rather than only what  you can find out when you do the examination (by whatever means).

 In contrast, the BFO 
people would probably like a more balanced use/combination of the two 
approaches/ontologies. The page is still very structured, but at one 
point the ADL switches to some other formal language which may or may 
not allow complex statements such as the ones described in Ceusters and 
Smith (2010). Note that this more balanced approach may not necessarily 
lead to a better semantical interoperability of data captured by 
  

I think this is more or less implying the above. One of the things to be aware of is that in the ADL (due to the reference model) we have some low level structures, in particular:

class CLUSTER {
    inherit ITEM
    items: List<ITEM>
}

class ELEMENT {
    inherit ITEM
    value: DATA_VALUE
}

a few other classes like ITEM_TREE add a few semantics to CLUSTER & ELEMENT, but are essentially the same thing.

This model leads to structures like:

ITEM_TREE
    items
        CLUSTER
            items
                ELEMENT
                ELEMENT
        ELEMENT
        CLUSTER
            items
                ELEMENT
                ELEMENT
    etc


now, with archetyping, this gets meaning attached to it:

ITEM_TREE
    items
        ELEMENT [at0001] -- test name
        CLUSTER [at0002] -- specimen detail
            items
                ELEMENT [at0003] -- specimen type
                ELEMENT [at0004] -- collection procedure
        ELEMENT [at0005] -- test status
        CLUSTER [at0006] -- macroscopic findings
            items
                ELEMENT [at0007] -- feature
                ELEMENT [at0008] -- colony count

Now the interesting thing here is that the bold meanings correspond to things in a realist ontology, whereas the underlined meanings correspond to relationships in a realist ontology. This is interesting because it is reference model objects in both cases being annotated to stand for relationships and things being related. Many archetypes are full of such structures; and if tools where BFO aware, they might be able to track down the right relationships and entities to act as candidates for the archetype models.

different groups of health care professionals. If the reality of the 
HCPs is to far apart, the ontologies they use, even if they follow the 
BFO guidelines, will be very orthogonal to each other and the data they 
describe might not be easily integrated. Hopefully, these realities 
overlap, and so will the terms and archetypes used at different 
locations of care delivery.

That's it. I hope these points are useful (they were for me), and that 
they show that the different approaches, all very valuable of course, 
involving decades of work, are closer than it appears, and will 
hopefully yield real benefits to health care, whether they're used 
independently or combined in a more or less balanced way.
  

I think this is a good discussion, thanks for the stimulating input.

- thomas beale

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