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Re: One ontology schema - heterogeneous instance bases

From: Xiaoshu Wang <wangxiao@musc.edu>
Date: Mon, 10 Sep 2007 12:48:49 +0100
Message-ID: <46E52F21.6080103@musc.edu>
To: Andrea Splendiani <andrea.splendiani@univ-rennes1.fr>
CC: Nigam Shah <nigam@stanford.edu>, satya30@uga.edu, public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org

Andrea Splendiani wrote:
>> The reason, I guess, that "biopax:AUTHORS", is developed is because 
>> the bioPAX people wants it to be a "format" rather making it a 
>> knowledge. 
> No... just DC was not so widespread and known when biopax begun, I guess.
Dublin Core starts at mid-90s. And bioPax at about 2002.  Even in RDF 
there were dublin core vocabulary. That is not a good guess, :-) Andrea.
>> To make it a format, you then think it in a closed world because you 
>> want to "control" your own terminology.  Ontology is different, its 
>> development is based on an open world semantics (at least RDF/OWL 
>> are).  When you developed your term, you should only care about the 
>> consistency of your terms and not the completeness.  And don't worry 
>> those terms that are not in your domain, for instance, I don't think 
>> AUTHORS are pathway knowledge.  If you have to use it for your 
>> application, then reuse other people's ontology. If there isn't any, 
>> develop your own but at least put them under a different namespace so 
>> you can later switch to others.....
> Yes I agree and I agree that "format" and "ontology" should be "more 
> distinct". 
> What I think is that we should have an "ontology of how a pathway is 
> represented" and a definition of a "valid unit of information 
> exchanged between two pathway systems". For the latter, you need some 
> constraint that usually involves a closed world assumption. But this 
> doens't mean you cannot base this on the URIs of the ontology (though 
> the discussion here gets more articulated).
You should focus on how a pathway is "described", not represented.  I 
don't think you understand the difference between open and close world 
semantics yet. See later.

> First, to understand the current biopax design, think about it in 
> Object Oriented terms, not OWL. Think about classes and slots. OWL was 
> largely used "as if it was" an OO specification.
Oh, please don't think it in OO term.  Most OO is based on a closed 
world semantics.  Let's use Java as an example, with the following class 

public class Foo {
   public void bar();

What will happen if you do something like this
    new Foo().notBar().

You get an error because notBar is not defined.

But if you make a similar ex:Foo class in RDF and constrain it to must 
have a bar property.  You sure can say things like,

_:x a ex:Foo;
     ex:bar _:bar.

But, you can still say the "_:notBar" thing about the Foo instance.

_:x _:notBar _:notBar.

So, please DO NOT think an ontology in OO.  (A slot is different but I 
prefer to use the RDF term 'property' since we are talking about RDF/OWL 
not frame. Again don't let's your ontology editor, in this case it is 
Protege, dictate your thinking as well.)
> By the way, you may note that a "pathway exchange" language with 
> "pathway" beining something as metabolic/signalling/interaction... was 
> clearly a underestimation of the task.
Sure, you can tailor your term with a specified interpretation.  Just 
like MGED ontology, which just simply convert OO terms into ontology 
term.  Isn't it odd that all MGED term has a superclass of 
mged:Ontology? So, an mged:Experiment is also an mged:Ontology.  But 
their interpretation is this, a mged:Experiment is not an experiment in 
the normal sense, it is the mged interpretation of the experiment.  
Well, with this "interpretation", it sure makes sense to make an 
mged:Expreiment a mged:Ontology because what they are modeled is not the 
real-word entity but an indirected interpretation of a real world 
entity.  Of course, you can do that.  But the problem is, how other 
people should use the mged term?  How others should interprets the 
"interpretation" of a mged term? And how two people's interpretation 
will be the same?

Hence, if the development of bioPax follows the similar path to create a 
"representation" of pathway knowledge, it falls to the same trap.  It is 
my sincere wish that the group don't think it in that way.

But if  bioPax's objective to develop a "special representation" of a 
pathway rather than a description of a pathway, I think developing XML 
schema is much more appropriate for the task because an XML document can 
be validated if a given document is correctly represented or not.


Received on Monday, 10 September 2007 11:49:56 UTC

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