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Re: proposal for standard NCBI database URI

From: Mark Wilkinson <markw@illuminae.com>
Date: Fri, 12 May 2006 07:32:57 -0700
To: "Xiaoshu Wang" <wangxiao@musc.edu>, public-semweb-lifesci@w3.org
Message-ID: <op.s9fz07g8nbznux@wayyye>

I may be completely missing the point of this discussion, but I don't see  
the point of this discussion :-)

What is represented by a URI is not defined by any convention or standard,  
and we shouldn't be trying to define it in this group.  rdfs:type can tell  
us what the situation is at the moment we need to know it... and  
hoepefully the range of the rdfs:type is controlled by an ontology in  
which we specify whether we are talking about a gene instance (i.e. the  
gene in a particular patient) or a gene instance (a particular DNA  
sequence) or a gene instance (a functional unit of heredity) or a gene  
instance (a set of letters and numbers representing a functinal unit of  
heredity), etc etc etc...  What constitutes an "instance" is in the eye of  
the beholder, surely...??

Excuse me if I am speaking out-of-turn, or simply missing the point  
entirely... it would't be the first time!

Cheers all!


On Thu, 11 May 2006 18:57:01 -0700, Xiaoshu Wang <wangxiao@musc.edu> 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.
> My point is: the existence of an URI doesn't imply that you have to use
> them. Of course, gene type is important, but under certain circumstances,
> there will be need of URIs for individual genes. For example, if you  
> were a
> structure biologiest who wants to compare the 3D structure of the a  
> protein
> under different physilogical condition, gene type won't be sufficient.  
> Or,
> if you were a anatomist, you probably won't be interested in any
> gene-related concepts at all.  There should not be any "rules" to  
> "govern"
> or "discriminate" concepts in terms of URIs.  It will be largely  
> determined
> the application context.  Of course, the more general a concept or (URI)  
> is,
> the more sharable it will be.  But on the other hand, the less specific
> action it will drive an application.
>> 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?
> In that particular case, what the URI represent is irrelevant.  The  
> point I
> wanted to make in the original message is try to say that we shouldn't  
> use
> the URI of an electronic record to represent the "resource" that is
> described by the record.
> Cheers,
> Xiaoshu
Received on Friday, 12 May 2006 14:33:01 UTC

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