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

Re: proposal for standard NCBI database URI

From: chris mungall <cjm@fruitfly.org>
Date: Thu, 11 May 2006 15:53:06 -0700
Message-Id: <07F81922-6351-4DE9-AF89-1449ECBC99D2@fruitfly.org>
Cc: <public-semweb-lifesci@w3.org>
To: Xiaoshu Wang <wangxiao@musc.edu>


On May 11, 2006, at 6:58 AM, Xiaoshu Wang wrote:

>
> --Chris
>> Genes should have their own URIs? That's some 10^16 or so
>> URIs just for the volume of space that I'm occupying right now.
>
> So what is the problem?  There are more concepts exist in the world  
> than
> each of us know. Does it limit ourself from living or learning or  
> working?
> The number of URI is unlimited, what is the big deal?  The issue is  
> not
> about space (by the way, how much space is a reasonable space  
> anyway), the
> issue is the design and management.

I guess I didn't make my point very clearly. I was attempting to get  
a clarification of whether we were talking about types of genes or  
instances

I think if you succeeded in RFID tagging every single gene instance  
in all my cells then allocating URIs for each would be a relatively  
trivial problem in comparison. But before we set about on that  
project I presume we'd first like to assign URIs to gene types such  
as "homo sapiens p53 gene"

>
>> More useful would be a URI for gene types - eg a URI for the
>> type "Homo sapiens p53 gene" (or an allele thereof).
>
> Ontologies should exist in any granuality and on any scale, saying  
> one type
> of ontology is more useful than another is arbitrary.  A pacifier  
> is very
> useful to my 10-month old son but completely useless to me.  Vice  
> versa is
> my laptop to him.

You wouldn't put a representation of your son's pacifier in an  
ontology. You would put a representation of the type "pacifier" in  
the ontology

>
> Having 10^16 or even 10^16000 genes doesn't matter. What matters is  
> how we
> can carefully modulizes the URIs so that we don't have to import those
> irrelevant concepts.

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.

So just to restate:

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?

>
> Cheers,
>
> Xiaoshu
>
>
>
Received on Thursday, 11 May 2006 22:53:15 GMT

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