W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > June 2007

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

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 31 May 2007 20:52:15 -0400
To: "Smith, Barry" <phismith@buffalo.edu>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, samwald@gmx.at, public-semweb-lifesci@w3.org, obo-relations@lists.sourceforge.net
Message-id: <465F6DBF.1080106@yale.edu>

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
>>
>>
>>
>>
>>
>> The information transmitted in this electronic communication is 
>> intended only for the person or entity to whom it is addressed and 
>> may contain confidential and/or privileged material. Any review, 
>> retransmission, dissemination or other use of or taking of any action 
>> in reliance upon this information by persons or entities other than 
>> the intended recipient is prohibited. If you received this 
>> information in error, please contact the Compliance HelpLine at 
>> 800-856-1983 and properly dispose of this information.
>
>
>
>
>
Received on Friday, 1 June 2007 00:52:42 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:48 GMT