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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Mon, 23 Mar 2009 13:41:19 -0400
Message-ID: <5639badd0903231041t43ba4c4m2516af7618e6502a@mail.gmail.com>
To: Peter Ansell <ansell.peter@gmail.com>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Peter, All,

On Sun, Mar 22, 2009 at 5:06 PM, Peter Ansell <ansell.peter@gmail.com> wrote:
> 2009/3/22 Oliver Ruebenacker <curoli@gmail.com>:
>>  There is an infinite number of possibilities. What is the criteria
>> for being relevant?
> The possibility I was referring to was the option for going through
> and defining the properties of the class of molecules as distinct from
> a random instance with instance specific variables. I would define the
> relevance of that method to be relative to the usefulness of the extra
> complexity involved in making sure that in each case the properties
> assigned to the random instance of the class were specific/precise
> enough to be more useful to scientists than the case where everything
> is placed as a property on the class of molecules. As you can't likely
> define all the configurations for a given instance of a complex
> molecular structure with respect to its environment, this would be
> difficult, but if you found an application that was grounded in a
> given environment it would be a possibility.

  I must have misunderstood you. I thought you were talking about not
making a commitment whether the world should be viewed through the
lens of a typical Systems Biologists (ensembles) or a Nano-Physicist
(single particles). My reply would have been that (a) Systems
Biologists already have such a hard time developing an ontology that
serves there own needs that serving other people's needs seems like a
luxury we can not afford and (b) should we consider other people's
needs, it is not clear which other people should have priority.

>>  Can you give an example?
> For example... How do you define a gene? Tough question I know, but do
> you define everything that can be transcribed as being a gene? How do
> you really associate genes across organisms considering mutations? If
> a gene acts as a promoter for its transcription in one gene but
> doesn't in another due to a mutation in the relevant upstream region
> can you really say the same sequence is the same gene? Even though its
> position in the intracellular space could still be the same, and its
> protein 3D conformation is still the same, there would be a duality
> where you would then have to redefine the gene as being a regulator
> for itself if you wanted to include its molecular functions inside the
> cell as part of its property set. It sounds counterintuitive to have
> to refer to the gene in two different ways just because in one
> organism its function didn't bind to its environment.
> One non-biological example I was referring to was the wave-particle
> duality for light, where if you wanted to be really in depth and
> define the light "thing", then you would either contradict yourself
> per current theory or you would create a dual distinct model that
> violated someones previous god-like decision that ":wave
> owl:distinctWith :particle"

  Sorry if I was not clear. I meant an example of how decisions you
consider "god-like" can be avoided. What is the alternative?

     Take care

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 17:41:55 UTC

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