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Re: Domain specific ontologies in the sciences

From: Phillip Lord <p.lord@russet.org.uk>
Date: 26 Jul 2004 11:48:03 +0100
To: "David States" <dstates@bioinformatics.med.umich.edu>
Cc: <public-semweb-lifesci@w3.org>
Message-ID: <vfu0vv3uzg.fsf@rpc71.cs.man.ac.uk>

>>>>> "David" == David States <dstates@bioinformatics.med.umich.edu> writes:

  David> Polymorphic definitions

  David> Molecular biologists sometimes joke that if you put 3
  David> scientists in a room and ask them to define a gene, you will
  David> get 5 definitions and 7 dissenting opinions.  Comedy often
  David> has its roots in reality, and there is considerable truth
  David> underlying this joke.  A gene might be a genetic locus
  David> without reference to a particular molecular structure, it
  David> might be a region of genomic DNA, or it might be specifically
  David> the transcribed exons, to name just a few possibilities.
  David> Often it is difficult to known in exactly what sense a term
  David> is being used.

  David> The point of this discussion is to point out that domain and
  David> range properties are often uncertain and may only be
  David> probabilistically assigned even with a domain.  RDF seems to
  David> define domain and range in absolute logical terms.  In
  David> applying RDF encoded semantic webs to the life sciences, it
  David> will be important to allow for uncertainty in meaning.

The semantic web is not going to provide some magic mechanisms for
removing doubt, uncertainty and confusion with biology. A pity,
because it would be nice if it did. 

It might, however, provide us with a technology for representing this
confusion in a standard syntax with a arguably clear semantics. 

In the case of polymorphic terms, I think it helps somewhat, as it all
of the semantic web technologies separate out the notion of a
resource, or concept, identifier and the noun phrase which is used to
describe that concept to the user. So we should be able to distinguish
between gene as "transcriptional bit of DNA" and "segregating unit of


Received on Monday, 26 July 2004 06:51:29 UTC

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