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RE: [Obo-relations] Advancing translational research with the Semantic Web (Not clear about definition of <is_location_of_process>)

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Fri, 1 Jun 2007 13:53:41 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D1244285E4@PHSXMB20.partners.org>
To: "William Bug" <William.Bug@DrexelMed.edu>, "Smith, Barry" <phismith@buffalo.edu>
Cc: <public-semweb-lifesci@w3.org>, <obo-relations@lists.sourceforge.net>
An OS process P2 could be described as a type of dependent continuant that come
into being when another process P1 instantiates it by making some OS-level call
which usually includes a pointer to the binary object that process will execute.

[VK] Is the process P1 above, a continuant or an occurrent? I ask this with the
intention of getting a better feel for BFO. In general learning by familiar
examples works well for me.


To get back to Matthias's original request:

At least using the OBO Relation definitions of 'located_in' and 'contained_in',
I believe you'd have to rephrase your relation as:

          <A> <contains_process> <B> means that <A> contains all of the
participants that make up process <B>.


[VK] I have issues with the word "all" above. What if the process is a
distributed process being executed by different participants in different
locations at a particular point in time?

In that case, how would the location of a process be determined? Maybe such a
situation doesn't arise for a biological process?


This may be one of the issues at the heart of what you are trying to clarify
here with this proposal.  Is the space within which ALL continuants of a given
process reside a material or immaterial continuant.  I believe more often than
not (possibly always), it will be latter.  For instance, ALL are the continuants
involved in the "Na+-K+ ATPase regeneration of ionic gradients" process that
follows the firing of an action potential - within what entity are they
contained?  There are elements in the cytoplasm, the plasma membrane, and the
extracellular space.  It seems as opposed to defining <A> (re: <A>
<contains_process> <B>) as being an aggregate object of those material
continuants, you would have an easier time asserting <A> is the bfo:Site where
those material continuants reside.


[VK] This partially answers the question above. I think the key is whether you
are seeking <process-location> or <process-region>

In the question raised earlier, it might be more useful to model it as
<process-region> as opposed to <process-location> ?





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Received on Friday, 1 June 2007 17:55:13 UTC

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