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Re: [Obi-function-branch] Instrument Function collection - Feedback
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From: Bill B. <wb...@nc...> - 2008-03-28 16:42:30
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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. >>>> Version: 7.5.519 / Virus Database: 269.22.0/1344 - Release Date: >>>> 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 |