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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Mon, 30 Mar 2009 09:15:46 -0400
Message-ID: <5639badd0903300615r49c3a1a0r76f7601b8db33052@mail.gmail.com>
To: Pat Hayes <phayes@ihmc.us>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello Pat, All,

On Sun, Mar 29, 2009 at 11:23 PM, Pat Hayes <phayes@ihmc.us> wrote:
> On Mar 29, 2009, at 10:48 AM, Oliver Ruebenacker wrote:
>>  Perhaps the question should read: What would you advice to some one
>> who wants to build an ontology to describe pathways for Systems
>> Biology purposes?
> I really have no advice to give, as I know virtually nothing about systems
> biology. My remarks were based on your raising the topic of statistical
> ensembles, which is enough to make me want to go and do something else, I'm
> afraid.

  There is no reason to be scared of statistical ensembles!

  Forget for the moment about Systems Biology and think of Science in general.

  A scientist applies a method to obtain results. Talking about the
method means talking about things particular to the discipline and the
tools used (e.g "On March 14, I placed the soccer ball on my table and
held my yellow ruler next to it.").

  The results can also be expressed in this language (e.g. "My yellow
ruler read 27.3 inches when held next to the soccer ball on my
table"), which is useful for those interested in the method, but it is
not required for those only interested in the results. In fact, if we
want to collect, combine and compare results obtained by different
methods, details particular to methods are usually counter-productive
(ruler? measuring tape? caliper? laser? red? yellow? table? chair?).
The consumer of the results is typically interested in a statement
such as "the diameter of a soccer ball is 27.4 inches plus-minus 0.3
inches". An expectation value and a variance.

  But what does the "diameter of 27.4 inches plus-minus 0.3 inches" in
above statement inhere in? Certainly not one particular soccer ball.
How about the set of all the soccer balls in the world? But why would
we be interested in all the soccer balls in the world? What if in some
strange place, people produce soccer balls of unusual sizes, would
that change the result for us?

  What we really mean when we say that a soccer ball has a diameter of
such and such, is that we imply that there are standard ways to obtain
soccer balls (e.g. going to the next sports store and buying one, or
taking one from the equipment room of the next gym, or participating
in a soccer match), and that these ways are equivalent in the expected
results. So there will be a range of possible scenarios (e.g. a soccer
ball of 27.2 inches, a soccer ball of 27.342 inches, a soccer ball of
9*pi inches, etc.) and each outcome comes with a probability. These
probabilities are usually not all the same, and since the number of
possible scenarios is typically infinite, it makes no sense to assume
they are. The probability distribution over the set of possible
outcomes is a ensemble.

  Enter Systems Biology. Systems Biology is a consumer of results from
many disciplines. Its objective is to put together results obtained by
a wide range of experimental, theoretical and computational methods in
Biological Physics, Molecular Biology, Physical Chemistry,
Biochemistry, Computer Science and Applied Math. Some of these methods
involve tracking single molecules, of definite sets of molecules. Some
do not. so Systems Biology needs a language to talk about these
results without referring to artefacts of methods used, which is the
language of ensembles.

     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, 30 March 2009 13:16:24 UTC

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