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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Wed, 25 Mar 2009 08:01:45 -0400
Message-ID: <5639badd0903250501g7b212571p7ee5b5af27a7d579@mail.gmail.com>
To: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>
Cc: Michel_Dumontier <Michel_Dumontier@carleton.ca>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Wacek, All,

  It is quite common to use terms from two different domains
interchangeably, if there is a natural isomorphism between the two
domains. I am sure every one on this list has at some point used
references to functions and function equations interchangeably and it
has not caused any harm (except maybe in a math exam where knowledge
about this distinction was tested).

  For every well-formed record, there is the set of all those
molecules or compounds the record is about. Two well-formed records
are equivalent, if they are about the same set.

  That makes a natural isomorphism between equivalence classes of all
well-formed records that can be possibly generated and all those sets
of molecules or compounds any of these records are about.

  This isomorphism has a sub-isomorphism between equivalence classes
of actually existing well-formed records and all those sets of
molecules or compounds they describe.

  Further, for any set of molecules or compounds that can be
identified by a finite piece of information, I can create a
well-formed record that contains this piece of information and is
about that set. Therefore, the isomorphism covers all relevant cases.

  The practical problems with records are primarily these:

  (1) A record is ambiguous on whether it
    (1a) is about a particular set of molecules or compounds
    (1b) is equivalent to a particular other record
  (2) a record about a particular set is desired but none exists for this set
    (2a) in particular places
    (2b) anywhere known

  These problems are not caused by using references to records and
entities interchangeably, and are not solved by making the distinction
clear. Rather, they can only be solved by creating more or better

     Take care

On Wed, Mar 25, 2009 at 7:16 AM, Wacek Kusnierczyk
<Waclaw.Marcin.Kusnierczyk@idi.ntnu.no> wrote:
> Michel_Dumontier wrote:
>> 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.
> hmm, since a biomolecule and a database record are actually different
> (or?), there seems to be, following your statement, a pragmatic reason
> to make explicit the distinction between them.
> what we know about them is yet another issue.
> vQ

Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
Received on Wednesday, 25 March 2009 12:02:25 UTC

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