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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