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

From: Smith, Barry <phismith@buffalo.edu>
Date: Thu, 31 May 2007 19:26:59 -0400
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
Cc: <samwald@gmx.at>,<public-semweb-lifesci@w3.org>, <obo-relations@lists.sourceforge.net>
Message-Id: <20070531232848.NXIE20106.mta9.adelphia.net@LENOVO-B1AD6243.buffalo.edu>

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

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

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:

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Received on Thursday, 31 May 2007 23:41:47 UTC

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