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

From: William Bug <William.Bug@DrexelMed.edu>
Date: Thu, 31 May 2007 21:32:25 -0400
Message-Id: <3D006702-F860-42A6-96A3-154BF836BD29@DrexelMed.edu>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, public-semweb-lifesci@w3.org, obo-relations@lists.sourceforge.net
To: "Smith, Barry" <phismith@buffalo.edu>
Maybe I'm reading this wrong, but I think we just have a nomenclature  
problem here.

The particular process Vipul has chosen here - an OS process  
executing a particular piece of binary code - is in fact a  
"continuant" in BFO speak, not a bfo:process.

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.

The act of instantiating the OS process is a bfo:process which - in  
the example above - would involve the following continuants (at a  
minimum): P1, P2, the OS-level code used to instantiate the process -  
and other such machine level continuants such as the Process Counter,  
the CPU execution modules, IO modules, etc.

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>.

In RO, located_in is a relation that pertains to two material  
continuant instances - e.g., c1 and c2 - with a precise  
mereotopological relation to one another - where the following:
	c1 located_in c2
entails:
	- c1 located_in c2 at a specific time t
	- at that time t, c1 is contained_in spatial region r1 , c2 is  
contained_in spatial region r2 is a subset of spatial region r1

For relations between material and immaterial continuants the  
mereotopological relation defined in OBO RO is 'contained_in' - e.g.,  
blood is contained_in blood_vessel_lumen, lung is contained_in  
thoracic_cavity.

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.

To be honest, however, I'm not certain which is more appropriate in a  
BFO context.  I believe this would depend on your particular Use Case  
- e.g., what do you intend to do with the resulting representation.

Cheers,
Bill


On May 31, 2007, at 7:26 PM, Smith, Barry wrote:

> At 04:56 PM 5/31/2007, Kashyap, Vipul wrote:
>
>>>> 1. Does the presence of all participants of a process at a location
>>> enough to
>>>> define the presence of a process at a location?
>>>
>>> Sounds reasonable to me.
>>
>> [VK] This probably is a consequence of the way you define a
>> biological process.
>>
>>>> 2. I do not claim to understand the OBO definition of a biological
>>>> process, but
>>>> from a computer science point of view, a process running on a
>>>> computer can have
>>>> states, e.g., activated, terminated, suspended, waiting-for- 
>>>> event, etc.
>>> These
>>>> states may correlate to some aggregation of states of  
>>>> participants in the
>>>> process. But I am not sure of the reason why a process cannot  
>>>> have a
>>> state?
>>>
>>> It is (it seems to me) the program or algorithm or plan (all
>>> continuants) which is activated.
>>> If a process is suspended or terminated, then surely the process is
>>> not there any more.
>>
>> [VK] OK that clarifies some of the issues and raises some others.
>> For instance:
>> - A computer process is indeed activated, suspended or terminated  
>> when the
>> execution of the program is activated, suspended or terminated.
>
> These terms ('activated', etc.) then mean different things; the
> question is: which is the primary meaning.
>
>> - Disagreement: A process in a suspended state (or according to  
>> you where all
>> the participants are in a suspended state) still exists.
>
> The life process, for instance, in cryogenics?
>
>> - An interesting corollary is that the execution of a program  
>> needs to be
>> distinguished from a program (please feel free to fill in the  
>> biological
>> equivalents).
>
> This is the basis of BFO's discussion between realizable entities
> such as functions and the processes which are their realizations; the
> former are continuants, the latter are occurrents.
>
>> - A process comes into existence only when a computer program  
>> executes.
>
> A process of a certain kind ...
>
>> - The last statement suggests that a process is more than the "sum  
>> of its
>> participants"
>
> Of course.
>
>>> And processes do not wait; people (for example) wait.
>>
>> [VK] Processes do wait for messages or events from other processes.
>
> This is just a figure of speech; in fact the device waits.
>
>>  For instance
>> the process1 = execution of the web browser program; waits-for
>> messages from process2 = execution of the web server program.
>
> Again, you are confusing the device which executes with the process
> which is the execution. The device waits.
>
>>> This terminology of 'states' is not, it seems to me,  
>>> ontologically clear.
>>
>> [VK] In attempt to clarify further, a state of a computer process =
>> state of the
>> execution of the computer program at a given point in time.
>
> This does not help, I'm afraid.
>
>> Also, it would be a big help if you can provide me with  
>> ontologically clear
>> terminology of 'states of process participants'.
>
> In fact, precisely because of the confused use of 'state' in so many
> quarters, BFO recommends that it not be used at all. But for all that
> you could want in this connection see:
> http://www.ifomis.uni-saarland.de/bfo/
> BS
>
>> Cheers,
>>
>> ---Vipul
>>
>>
>>
>>
>>
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Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu
Received on Friday, 1 June 2007 01:30:13 GMT

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