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Re: blog: semantic dissonance in uniprot

From: Bijan Parsia <bparsia@cs.man.ac.uk>
Date: Mon, 30 Mar 2009 17:18:19 +0100
Message-Id: <A085CAF1-533F-45B1-A874-F0376BA6EDE1@cs.man.ac.uk>
To: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
On 30 Mar 2009, at 17:04, Oliver Ruebenacker wrote:

>      Hello Bijan, All,
>
> On Mon, Mar 30, 2009 at 11:39 AM, Bijan Parsia  
> <bparsia@cs.man.ac.uk> wrote:
>> On 30 Mar 2009, at 16:23, Oliver Ruebenacker wrote:
>>>  That is probably the most used phrase in the Semantic Web  
>>> community.
>>
>> And least adhered to?
>
>   Most used as an empty cliche.

I certainly wasn't using it that way, as, believe, my concrete  
examples showed.

>> What's your problem with providing application requirements?
>
>   None, but that was not the topic.

You asked for advice. I gave what I needed in order to give you advice.

>>>  I have no idea what that paradigm is.
>>
>> http://portal.acm.org/citation.cfm? 
>> id=1064.1066&coll=GUIDE&dl=GUIDE&CFID=15151515&CFTOKEN=6184618
>   Still no idea.

Because? You could read it? You couldn't get it? You don't care to?

ASK/Tell (i.e., characterizing a KR system functionally in terms of  
questions answered in response to information "told" to the system)  
is pretty bog standard.

>>>  An ontology should be independent of a particular application.
>>
>> First, there's a big difference between being tied to a particular
>> application and being informed by intended applications. I  
>> sincerely doubt
>> the general utility of an ontology designed without *any* thought  
>> to the
>> class of applications for which it is intended to be used. Advice  
>> that is
>> not at all informed by the broad characteristics of the  
>> applications for
>> which the ontology shall be used is worthless.
>
>   Class of applications = Systems Biology applications

That's not a useful description. It doesn't give any application  
features.

For example, an editor for descriptions of Systems Biology  
experiments is very different than a computer aided tutotiral.

>> As far as I can tell it's a format converter and visualizer. No  
>> ontologies
>> needed at a first approximation.
>
>   Uses an ontology to integrate BioPAX and SBML. If you know an
> alternate way, you should publish.

Isn't the issue *how* it does that integration?

But I see we can't productively interact, so I regret having  
responded and will now stop.

Cheers,
Bijan.
Received on Monday, 30 March 2009 16:14:34 UTC

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