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Re: blog: semantic dissonance in uniprot

From: Bijan Parsia <bparsia@cs.man.ac.uk>
Date: Mon, 30 Mar 2009 16:31:31 +0100
Message-Id: <B6C1DC61-F6F3-4C3E-BA00-BDD46967DABC@cs.man.ac.uk>
To: public-semweb-lifesci <public-semweb-lifesci@w3.org>
On 30 Mar 2009, at 16:12, Oliver Ruebenacker wrote:

>      Hello Bijan, All,
>
> On Mon, Mar 30, 2009 at 7:35 AM, Bijan Parsia
> <bparsia@cs.manchester.ac.uk> wrote:
>>>  Isn't that the typical way, that ontologies define classes and
>>> properties and users of these ontologies instantiate these classes?
>>
>> Nope. It's "a" way, but it's hardly typical and the way you talk  
>> about it is
>> seriously misleading.
>
>   Can you name any popular ontology that does not primarily declare
> classes and properties?

I don't have to, since I'm not claiming that.

[snip]
>> So, that's just not a helpful way to think about things in the owl  
>> context.
>> I myself do use the "TBox=schema; ABox=data" analogy sometimes,  
>> but I fear
>> that its utility is limited and risk of misinterpretation very high.
>
>   It's not an analogy. It's a typical use.

The problem is that "schema" and "data" have strong connotations  
which don't hold for OWL ontologies.

>> Second, there's lots of ways to use ontologies with out having to use
>> logical constants (i.e., individuals). Alignment of database  
>> schemas comes
>> to mind. There you might never lift the database data into the  
>> ontology, but
>> merely use information from the alignment to rewrite queries.
>
>   You mean, you rewrite queries never to be run?

No, who said that?

> Then, what are you
> rewriting them for?

You're rewriting SQL queries, not SPARQL queries.

>> That's not to say that anyone writes class descriptions intending  
>> them to be
>> necessarily empty (i.e., unsatisfiable). Just that instance  
>> retrieval is one
>> task among many.
>
>   I wasn't talking about tasks, but of a pattern I found almost all
> ontologies I have seen so far to conform to. Instead of philosophizing
> about it, why don't you just show me a popular ontology that does not
> fit that pattern?

NCI thesaurus.

Cheers,
Bijan.
Received on Monday, 30 March 2009 15:27:47 UTC

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