Re: seeks input on Study Data Exchange Standards

Again, in real life as we do this, we are really talking about SNOMED with 
it's EL+ logic.  It's like OWL without negation or disjunction.
We only have SNOMED associated with a few nodes in a model, usually the 
ones that would indicate the diagnosis or what procedure was done.

The idea of labels would be to make what we do explicit (we know what we 
do but how would you happen to know) and generalize it so that in the 
future if anyone needed another ontology for another purpose they could 
add it to their model.

You mentions something I wonder about.  If you lock the ontology (for 
example this is a release of SNOMED and you cant add new terms), and you 
run the reasoner and store all the inferred triplets as RDF along with all 
the stated ones,  then could you really do just SPARQL at that point and 
not need a reasoner?



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"Matthias Samwald" <matthias.samwald@meduniwien.ac.at> 
08/22/2012 04:05 AM

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<meadch@mail.nih.gov>, Peter Hendler/CA/KAIPERM@KAIPERM
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<kerstin.l.forsberg@gmail.com>, <public-semweb-lifesci@w3.org>
Subject
Re: seeks input on Study Data Exchange Standards






Peter wrote:
> Using both SQL and subsumption you can automatically find things like 
this: 
> "find all disorders that are a kind of adverse drug reaction where drug 
is a subtype of antibiotic and was given for a kind of gram negative 
bacterial infection of the digestive system". 
Simple subsumption such as that can be inferred by basic, RDFS-type 
reasoning. I don't see any potential problems caused by OWL's open world 
assumption here (please point them out if there are any).
Indeed, the open-world assumption of OWL can make creating expressive 
ontologies and using reasoners tricky. However, I do not see why the same 
should be true for using RDF, basic RDFS subsumptions and SPARQL. Could 
you provide some examples?
 
If we wanted to use more expressive ontologies with "intensional" entities 
(i.e., defined classes) in the overall system, we could simply run a 
reasoner and materialize the inferred statements for each ontology before 
it is 'shipped' for use by other systems. These other systems could then 
use simple RDF(S) and SPARQL (and maybe SPARQL rules), without the 
performance issues and potential unexpected consequences of open-world 
reasoning with expressive OWL ontologies. Specifying if and how exactly 
each specific node should be reasoned upon sounds so complex that I cannot 
imagine it working in any practical setting.
 
Best,
Matthias