Hi Barry,
Welcome to the SWHCLS list. Such a discussion reminds me of the Nature
paper: "Are the current ontologies in biology good ontologies?"
(http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html). The
paper uses the MGED (microarray) ontology to illustrate some of the
ontological issues. I'm just curious how the BFO principles and practice
can help make such a microarray ontology more ontologically sound and
therefore more machine readable. In the context of neuroscience, I
wonder if we can look at how to convert some of the public data (or
metadada) extracted from the NINDS Microarray consortium
(http://arrayconsortium.tgen.org/np2/home.do) into some kind of OWL
ontology. Perhaps some MGED and/or HCLS folks are also interested in this.
Best,
-Kei
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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