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Re: proposal for standard NCBI database URI

From: chris mungall <cjm@fruitfly.org>
Date: Fri, 12 May 2006 04:59:17 -0700
Message-Id: <0C54D7B9-CBCC-4738-873D-F53941E38BB8@fruitfly.org>
Cc: <public-semweb-lifesci@w3.org>
To: Matthias Samwald <samwald@gmx.at>

On May 11, 2006, at 4:18 PM, Matthias Samwald wrote:

>>  Hmm, the 10^16 genes instantiated in the volume of space occupied
>>  by me are neither irrelevant (to me anyway), nor are they concepts.
>>  They are very real instances of physical material objects - at
>>  least under one definition of gene.
>>  in your example I presume the ID gene/123 was intended to be an ID
>>  for a gene type rather than an instance - or perhaps not?
> It could also be a URI for an OWL class. The 10^16 genes (in the  
> 'physical object' sense) in your body would be instances of this  
> class - we would probably never make this instances, though. Using  
> classes would be the most consistent way to do it.


> However, I am not an advocate of doing everything with OWL classes,  
> as it is hard to implement - actually I am very opposed to that  
> idea. I am preferring a two-world approach: unifying realist  
> descriptions of spatiotemporal particulars (e.g. one of your genes)  
> with conceptualist descriptions (e.g. the concept of 'human insulin  
> receptor gene'). In this model, the conceptual description are used  
> to annotate the realist descriptions. However, I will write more  
> about that some other time, as this is not the topic of this  
> discussion.

I agree that OWL classes would present many implementation  
difficulties here. I'm interested in what the alternatives are, given  
that I think we both want to avoid unnecessary abstractions such as  
"instance of a database record". I'm wondering how your concept of a  
conceptual description differs from owl classes or from my types.

> Either way, aiming to describe mere concepts (and not the 'real  
> things' themselves) is still much better than simply describing  
> database entries and their relations to one another. If we just  
> want to have better interoperability between database entries,  
> generic XML with XLink would suffice - there would be no  
> significant need for RDF or OWL, in my opinion.

I pretty much agree, with the caveat that I would include types as  
being real, and I'm more interested in types than concepts - but  
that's another discussion entirely


> //Matthias
Received on Friday, 12 May 2006 12:04:21 UTC

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