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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Mon, 23 Mar 2009 14:07:15 -0400
Message-ID: <5639badd0903231107s4b18aea2vb43380c4093c38d5@mail.gmail.com>
To: marshall@science.uva.nl
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Scott, All,

  Pardon my ignorance, but how exactly do we know that these
statements are wrong? Suppose the instance representing the fruit fly
protein is defined as a sequence pattern that matches a number of
proteins. Suppose isolatedFrom, applied to such a sequence pattern, is
defined as an organism from which proteins can be isolated that match
that pattern. Suppose, the same pattern matches proteins isolated from
both fruit flies and sporophytes. These look like perfectly reasonable
assumptions to me, and they would make the two statements true. Am I
missing something?

     Take care

On Fri, Mar 20, 2009 at 1:35 PM, M. Scott Marshall
<marshall@science.uva.nl> wrote:
> FYI:
> http://i9606.blogspot.com/2009/02/semantic-dissonance-in-uniprot.html
> I thought that the above blog entry would interest some of you (it
> apparently already has interested a few of you that have added comments :)
> ). The blog is from Benjamin Good (from Mark Wilkinson's Lab) and was
> referenced during a napkin discussion I had with Marco Roos and Ben about
> how one could best refer to a protein in text-mined triples. One of the best
> options seemed to be to use a PURL that referred to a record associated with
> the protein. Sound familiar? Those of you who have been with us for more
> than a year will think so. See http://sharednames.org for an attempt to
> approach the issue.
> -Scott

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Monday, 23 March 2009 18:07:51 UTC

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