W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2006

Re: proposal for standard NCBI database URI

From: Matthias Samwald <samwald@gmx.at>
Date: Fri, 12 May 2006 01:18:02 +0200
To: <public-semweb-lifesci@w3.org>
CC: <public-semweb-lifesci@w3.org>
Message-ID: <20065121182.371909@cqueberel>

> 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.

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.

Received on Thursday, 11 May 2006 23:18:11 UTC

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