Naming conventions

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The names of disorders in CVDO seem to be a mixture of

 1. X disorder
 2. <descriptor> X

I find the latter form confusing. I would expect "inflammated blood vessel" to 
be a subclass of "blood vessel" that has the quality of being inflammated.

However, your class is located in a blood vessel.

I would cautiously recommend reserving "<descriptor> X" to be names of 
subclasses of X, and to use a different form for disorders that are part of or 
located in X. "blood vessel inflammation disorder" is awkward but less 
ambiguous. I suppose "blood vessel inflammation" would be reserved for the 
ogms:pathological process.

I think OGMS should come with a guide on naming conventions.

This may all seem very nit picking but I think it will help further down the 
line. I have a suspicion there may be some lurking problems when you start 
adding equivalence axioms to the existing "inflammated X" classes.

[btw - change inflammated to inflamed?]

Original issue reported on code.google.com by cmung...@gmail.com on 15 Mar 2013 at 12:29

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There is indeed a general issue in OGMS concerning the connections between some 
disorders (like "inflamed blood vessel") and the corresponding anatomical part 
("blood vessel"), which comes from the fact that disorders must be independent 
continuants (if I remember correctly, Ludger Jansen suggested that disorders 
could instead be qualities). Here, this is a case where it would seem simpler 
to have a quality (inflamed) as a disorder, but that’s not OGMS approach.

As you noticed, we chose most of the time a very general relation (more general 
than e.g. a parthood or is_a relation) between a disorder and its corresponding 
anatomical part, namely located_in. This way, even if we change the label of 
the disorder to something else, this relation would probably continue to hold. 
More specific relations (like parthood or is_a) can be added in the future when 
applicable.

We also wanted to respect the principle of single asserted inheritance – this 
is why we did not assert "inflamed blood vessel" as a sub-class of both 
"disorder" and "blood vessel". We could try to make such that one of these 
inheritances would be inferred, but this would require a heavier axiomatization 
than the one we have developed yet.

As you suggested, "blood vessel inflammation disorder" would fit better the 
role of disorder (by definition), but would be less informative, so on the long 
run I am not sure that this would be the best choice. Our choice of "inflamed 
blood vessel" should not be understood as a definitive position on this 
problem, but as a suggestion that could be improved and that raises questions 
about OGMS approach.

Original comment by adrien.b...@gmail.com on 15 Mar 2013 at 6:05

• Changed state: Accepted
• Added labels: Type-Enhancement
• Removed labels: Type-Defect

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- I'm not an expert on OGMS, I find the treatment of disorders as ICs 
confusing. In this case I'm not sure if in OGMS the disorder is part of the 
blood vessel (which part? How do we draw the boundaries?) or the blood vessel 
itself (which is different than how you have modeled it).

- it isn't true that located in is more general than is_a (it isn't really a 
well-formed statement in OWL, as SubClassOf is not an object property).

- if you do decide to model this such that "inflamed blood vessel" is a subtype 
of "blood vessel" then you do not necessarily have asserted MI. You model this 
as equivalentTo "blood vessel and has_quality some inflamed" and then you get 
inferred parentage to "inflamed vessel", "inflamed organ", "vessel with 
abnormality" etc. I'm not saying you should model it this way for now - if 
you're using OGMS you should use it in toto - ask the OGMS experts for help 
here.

- The no asserted MI thing has become dogma. IMHO the important thing is 
understanding how to use reasoners to do the classification work for you, and 
having you avoid recapitulating the work of anatomy ontology. See issue #1

- I see your point about the naming, my suggestion "blood vessel inflammation 
disorder" is horrible. But I think it is confusing how it is labeled right now. 
The label suggests one thing, the OWL another. Perhaps it could just be marked 
with a comment in the interim.

Original comment by cmung...@gmail.com on 15 Mar 2013 at 6:25