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Thanks, Barry.

I was also hoping that you and Alan could provide some feedback on the  
"BFO styled" Function definitions found on this Google spreadsheet:

	http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en

This is to ensure that the work they are doing to build these out -  
whether done by the Instrument OR the Planned Process/Protocol  
Application branch are in fact capturing what a BFO function needs to  
capture.  You can send such feedback directly to the OBI-Function  
mailing list, so we can be certain to have a documented record of all  
information relative to creating BFO-compliant function in one place
On Mar 28, 2008, at 7:29 AM, Barry Smith wrote:

>
>>>> Barry + Alan, please vet this:
>>>>
>>>>
>>>>
>>>> For each instrument I with function F there is a  
>>>> protocol_application P
>>>> that
>>>> has_participant instrument I which realizes function F as part of  
>>>> P.
>
> Better
>
>>>> For each instrument I with function F there is a protocol P each  
>>>> application of which
>>>> has_participant instrument I which realizes function F as part of  
>>>> P.
>
>
>
>
>>>> We can define the ‘minimal protocol application P F for  
>>>> instrument I’ as
>>>> the one for which there is no partial realization
>
> which
>
>>>> fully realizes the
>>>> instrument function F.
>>>>
>>>>
>>>>
>>>> We can then define a relationship:  instrument I ‘has minimal  
>>>> functional
>>>> realization‘ in protocol application PF. We can then later  
>>>> automatically
>>>> translate PF --> F (e.g. heating --> ‘heating_function’) to  
>>>> create the
>>>> instrument function hierarchy in parallel.
>>>>
>>>>
>>>>
>>>> If this or something similar is acceptable, the next step would  
>>>> be to
>>>> convert the function terms to Pf terms, and submit them to the  
>>>> protocol
>>>> application branch (if they don’t exist there already).
>
> I would need to see an example of such a hierarchy to be sure, but  
> it looks promising
> The reason for my first change, is that not all instruments in fact  
> get used
> BS
>
>
>
>
>>>> - Bjoern
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>  _____
>>>>
>>>> From: Bill Bug [<mailto:wb...@nc...>mailto:wb...@nc... 
>>>> ]
>>>> Sent: Monday, March 17, 2008 9:40 PM
>>>> To: Barry Smith; Alan Ruttenberg; Bjoern Peters; Melanie Courtot
>>>> Subject: Fwd: Instrument Function collection - Feedback
>>>>
>>>>
>>>>
>>>> Hi All,
>>>>
>>>>
>>>>
>>>> Your probably wondering why I've gathered you all here.
>>>>
>>>>
>>>>
>>>> I'm at a loss to know what to say or do regarding these instrument
>>>> functions:
>>>>
>>>>
>>>>
>>>>           HYPERLINK
>>>> "<http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en 
>>>> >http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en 
>>>> "http:/
>>>> /spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
>>>>
>>>>
>>>>
>>>> Here are the issues as I see them:
>>>>
>>>>
>>>>
>>>>           1) I thought we agreed at the Vancouver meeting that OBI
>>>> bfo:functions would be described during the process of specifying  
>>>> their
>>>> associated processes in the protocol application branch
>>>>
>>>>
>>>>
>>>>           2) Most of the functions listed here are verbs which  
>>>> implies
>>>> they are processes, not bfo:functions (e.g., measurement is the  
>>>> function,
>>>> measure is the process)
>>>>
>>>>
>>>>
>>>>           3) The definitions don't appear to capture what would be
>>>> required in BFO (I've made a feeble attempt to translate them into
>>>> BFO-speak
>>>> in the far right column, but that feels largely like just a  
>>>> matter of
>>>> syntax).
>>>>
>>>>
>>>>
>>>>           4) The granularity of the definitions varies widely -  
>>>> as I
>>>> expect functions may ultimately need to do.  However, it feels  
>>>> like: (a)
>>>> more systematic approach to granular definitions needs to be  
>>>> applied; (b)
>>>> the use of these functions needs to be better defined so as to  
>>>> better
>>>> understand what the definitions need to include.
>>>>
>>>>
>>>>
>>>>           5) Feels like examples are needed which demonstrate how  
>>>> or why
>>>> the definitions are important to the way in which these functions  
>>>> act to
>>>> relate a device to a process.
>>>>
>>>>
>>>>
>>>> Any thoughts/feedback you can offer would be greatly appreciated.
>>>>
>>>>
>>>>
>>>> Cheers,
>>>>
>>>> Bill
>>>>
>>>>
>>>>
>>>> Begin forwarded message:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> From: Daniel Schober <HYPERLINK
>>>> "<mailto:sc...@eb...>mailto:sc...@eb..."<mailto:sc...@eb... 
>>>> >sc...@eb...>
>>>>
>>>> Date: March 11, 2008 1:42:15 PM EDT
>>>>
>>>> To: Bill Bug <HYPERLINK "<mailto:wb...@nc...>mailto:wb...@nc... 
>>>> "<mailto:wb...@nc...>wb...@nc...>
>>>>
>>>> Cc: HYPERLINK
>>>> "<mailto:obi...@li...>mailto:obi...@li... 
>>>> "obi-instrument-branch@li
>>>> sts.sourceforge.net
>>>>
>>>> Subject: Instrument Function collection - Feedback
>>>>
>>>>
>>>>
>>>> Hi Bill,
>>>>
>>>> We (the instruments branch) are going through our upper level and  
>>>> collect
>>>> more important/general instrument functions for later crossproduct
>>>> generation. The function collection lives here:
>>>>
>>>> HYPERLINK
>>>> "<http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en 
>>>> >http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en 
>>>> "http:/
>>>> /spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
>>>>
>>>> Could you have a look at this, and possibly attend our next call  
>>>> on these
>>>> (Tue, 18.Mar 4 pm GMT) ?
>>>>
>>>> We would like to know your plans/next steps for the functions  
>>>> branch, and
>>>> would be happy to get feedback if what we cover (and how we cover  
>>>> it) in
>>>> the
>>>> spreadsheet is useful.
>>>>
>>>> Cheers,
>>>>
>>>>  Daniel Schober (on behalf of the instruments branch).
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ____________________________________________________________________________
>>>> ______________
>>>>
>>>>
>>>>
>>>> Dr. Daniel Schober
>>>>
>>>>
>>>>
>>>> NET Project - Ontologist
>>>>
>>>>
>>>>
>>>> The European Bioinformatics Institute   email:  HYPERLINK
>>>> "<mailto:sc...@eb...>mailto:sc...@eb..."<mailto:sc...@eb... 
>>>> >sc...@eb...
>>>>
>>>> EMBL Outstation - Hinxton               direct: +44 (0)1223 494410
>>>>
>>>> Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
>>>>
>>>> Cambridge CB10 1SD, UK                            Room: A3-141  
>>>> (extension
>>>> building)
>>>>
>>>>
>>>>
>>>> Project page: HYPERLINK
>>>> "<http://www.ebi.ac.uk/net-project>http://www.ebi.ac.uk/net- 
>>>> project"<http://www.ebi.ac.uk/net-project>www.ebi.ac.uk/net-project
>>>>
>>>>
>>>>
>>>> Personal page:    HYPERLINK
>>>> "<http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 
>>>> >http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 
>>>> "htt
>>>> p://<http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 
>>>> >www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
>>>>
>>>> Former home page: HYPERLINK
>>>> "<http://www.bioinf.mdc-berlin.de/%7Eschober/>http://www.bioinf.mdc-berlin.de/%7Eschober/ 
>>>> "<http://www.bioinf.mdc-berlin.de>http://www.bioinf.mdc-berlin.de
>>>> /%7Eschober/
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> William Bug, M.S., M.Phil.
>>>> email: HYPERLINK "<mailto:wb...@nc...>mailto:wb...@nc... 
>>>> "<mailto:wb...@nc...>wb...@nc...
>>>>
>>>> Ontological Engineer
>>>> work: (610) 457-0443
>>>>
>>>> Biomedical Informatics Research Network (BIRN)
>>>>
>>>> and
>>>>
>>>> National Center for Microscopy &
>>>>
>>>> Imaging Research (NCMIR)
>>>>
>>>> Dept. of Neuroscience, School of Medicine
>>>>
>>>> University of California, San Diego
>>>>
>>>> 9500 Gilman Drive
>>>>
>>>> La Jolla, CA 92093
>>>>
>>>>
>>>>
>>>> Please note my email has recently changed
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> No virus found in this incoming message.
>>>> Checked by AVG.
>>>> Version: 7.5.519 / Virus Database: 269.21.7/1333 - Release Date:  
>>>> 3/18/2008
>>>> 8:10 AM
>>>>
>>>>
>>>>
>>>> No virus found in this outgoing message.
>>>> Checked by AVG.
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>>>> 3/26/2008
>>>> 8:52 AM
>>>>
>>>
>>
>> William Bug, M.S., M.Phil. email: <mailto:wb...@nc...>wb...@nc...
>> Ontological Engineerwork: (610) 457-0443
>> Biomedical Informatics Research Network (BIRN)
>> and
>> National Center for Microscopy &
>> Imaging Research (NCMIR)
>> Dept. of Neuroscience, School of Medicine
>> University of California, San Diego
>> 9500 Gilman Drive
>> La Jolla, CA 92093
>>
>> Please note my email has recently changed
>>
>>
>
>

William Bug, M.S., M.Phil.                                         			 
email: wb...@nc...
Ontological Engineer									work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
and
National Center for Microscopy &
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed

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