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Re: blog: semantic dissonance in uniprot

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Wed, 25 Mar 2009 10:41:37 +0000
To: "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
Message-ID: <87prg551ge.fsf@newcastle.ac.uk>

"Michel_Dumontier" <Michel_Dumontier@carleton.ca> writes:
> And I'm trying to explain that there is no pragmatic reason to make
> explicit the distinction between a biomolecule (and what we know about
> it) and a database record (and what we know about the biomolecule)
> unless they are actually different.  It just complicates things in a
> wholly unnecessary way. 


I've given a clear example. Where two databases exist, with two records,
which appear to be referring to the same (class of) molecules. 

The problem remains, however, that we have no clear and unambiguous way
of defining what we by "the same molecule". So, we refer to a database
which brings along with it an (often ad hoc) definition of what "the
same molecule" means.

We could, of course, produce a resource which gives identifiers to, say,
all the classes of proteins in the world. But this would not solve the
problem; it would just introduce yet another resource and another
methodology for defining what we mean by an individual protein. 

If I remember correctly the original post that started this of Ben has
it about right. We need some tags which say "these two database records
are about the same protein, well, sort of, at least in this case, for
the purposes of what I am doing".

This argument reminds me of when the genome sequences were being
completed and people were arguing about how many genes there are in
humans. Different groups had different pipelines and came up with
different answers; ultimately, you had to conclude that there were all
pretty close and that working out which was best was nearly impossible
in the absence of an exact answer, an exact definition of a gene. We
don't have one; let's get over it and deal with this as is. 

Phil
Received on Wednesday, 25 March 2009 10:42:13 UTC

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