W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > September 2007

Re: One ontology schema - heterogeneous instance bases

From: Xiaoshu Wang <wangxiao@musc.edu>
Date: Mon, 10 Sep 2007 11:07:57 +0100
Message-ID: <46E5177D.7020309@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:
>> Using RDF as an "exchange format" is just outright wrong.  How do you 
>> decide if an RDF document is in BioPAX format or not? I don't know 
>> how active BioPAX is now (their website shows the last conference 
>> call was more than two years ago). But such line of thought will doom 
>> (and have perhaps already doomed) their fate
> Hi, let me add my two cents o this thread.
> *) BioPAX is active, but its current "real" website is the wiki, not 
> the main site (link under "community"). Unfortunately, nobody had time 
> untill now to make this more explicit.
> That RDF is "outright wrong" as an exchange format is questionable. At 
> least we had the experience of RDF 1.0 in this direction. But I agree 
> that the distiinction between data and meta-data is not so clear.
The problem is not about what is data and what is metadata.  The problem 
is that how you think will dictate how you design your artifact.  In the 
case of data standard, it subsequently determines how much 
inter-operable your ontology is with others.

Let's use a concrete term as example, the biopax:AUTHORS.  (By the way, 
it is very strange that bioPAX, use Capticalized term for property and 
small-cased term for class, where the most conventions is the other way 
around). Is its semantics any different from the "creator" defined by 
the dublin core?  If there isn't any, (at least from what I can tell), 
then bioPAX SHOULD NOT reinvent the wheel to mint this term because, if 
every "ontology" developed its own author term, then, there will be 
hundreds of "authors/creators" etc., that we have to align when the 
so-called BioPAX data is mixed with other kind of data.  And if you 
think it doesn't matter, why bother developing ontologies, what is wrong 
with using XML schema then?

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.  
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 

If an ontology is developed to be a "format", it will fail and fail 


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

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