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Re: [Obi-instrument-branch] Obi-instrument-branch Digest, Vol 25, Issue 2
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From: Philippe Rocca-S. <ro...@eb...> - 2009-02-12 13:26:11
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Hi Oliver, as we discussed on the coord call yesterday, it is likely that monthly called will be held instead of weekly calls. We 'll have to agree on time slot and date: I guess we could retain the current time slot and set the call 2 weeks before the release dates (which are usually end of months) How does it sound ? All issues could be discussed on the list. Unresolved issues pushed to the call. Term submission could be made following the guidelines James pointed to in his recent post. (Note: there is a perl script written by Jay to parse those term templates into OWL classes, in the right location if a parent class is provided). Cheers Philippe Frank Gibson wrote: > Hi Oliver, > > We have currently suspended the instrument calls at the moment as we > have no branch leader and Melanie and I cant devote as much time as we > used to. We are currently editing the branch in are own time based the > current definintion of device. Are there specific instrument terms you > require for inclusion within OBI? > > Thanks > > Frank > > On Thu, Feb 12, 2009 at 11:32 AM, Yongqun He <yon...@me...> wrote: > >> Hi Frank and Melanie, >> >> I would like to help edit the instrument branch. I am still new to OBI and >> would like to contribute more. As a junior faculty here in Michigan, I still >> have flexible time to do some research I enjoy doing. >> >> When is the instrument branch call time? >> >> Oliver >> >> Yongqun "Oliver" He, DVM, PhD >> Assistant Professor >> Unit for Laboratory Animal Medicine >> Department of Microbiology and Immunology >> and Center for Computational Medicine and Biology >> University of Michigan Medical School >> Office: Room 105, Animal Research Facility (ARF) >> Mailing: 018 ARF, 1150 W. Medical Center Dr. >> Ann Arbor, MI 48109 >> Email: yon...@um... >> Tel: 734-615-8231 (O); 734-615-2455 (L) >> Fax: 734-936-3235 >> http://www.ulam.umich.edu/academic/he.htm >> http://www.med.umich.edu/microbio/bio/he.htm >> http://www.hegroup.org/ >> >> >>>>> <obi...@li...> 2/12/2009 02:34 >>>>> >> Send Obi-instrument-branch mailing list submissions to >> obi...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >> or, via email, send a message with subject or body 'help' to >> obi...@li... >> >> You can reach the person managing the list at >> obi...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Obi-instrument-branch digest..." >> >> >> Today's Topics: >> >> 1. Re: instrument calls (Alan Ruttenberg) >> 2. Re: instrument calls (Frank Gibson) >> 3. Re: instrument calls (Trish Whetzel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 10 Feb 2009 04:31:29 -0500 >> From: Alan Ruttenberg <ala...@gm...> >> Subject: Re: [Obi-instrument-branch] instrument calls >> To: Trish Whetzel <plw...@gm...> >> Cc: obi...@li... >> Message-ID: >> <29a...@ma...> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Another question forgot to ask. How does it interact with imports? We need >> the imports to reason correctly (and because parts are defined in different >> branches). We also need to be able to control to which branch edits are >> made. >> Finally, if we do try this it needs to be done in a way that supports our >> version management - after some session of work, either collaborative or >> individual, the branch that is edited needs to be checked in. >> >> -Alan >> >> On Mon, Feb 9, 2009 at 9:10 PM, Trish Whetzel <plw...@gm...> wrote: >> >> >>> Since it sounds like you will need to intersperse conversations with >>> changes to the owl file, would use of Collaborative Protege be helpful? >>> >>> Here are answers to questions brought up at the OBI workshop: >>> 1) Can it do reasoning? >>> Yes. >>> >>> 2) Can it save all versions? >>> The edits are simultaneous in Collaborative Protege. There isn't really >>> the >>> concept of versions. Whatever change a user makes, all other users will >>> see >>> immediately. The ontology can be saved at any time in an OWL format and >>> can >>> be submitted to a SVN, if needed. >>> >>> 3) Can changes be rolled back? >>> No. It is dangerous to do that with simultaneous editing. New version >>> based >>> on Protege 4 has that in plan. >>> >>> 4) Is the OWL file accessible in case there are special edits that need to >>> be done offline that cannot be performed in Prot?g?? >>> Yes. >>> >>> 5) Can the file be locked similar to a svn lock so that if offline work is >>> needed, the file will be the same when added back to the server? >>> No. Edits are simultaneous, so there are no versions. This "locking" >>> feature is planned for the next version. >>> >>> 6) Is this an active project? >>> Definitely. >>> >>> >>> Trish >>> >>> >>> >>> On Mon, Feb 9, 2009 at 5:05 PM, Melanie Courtot <mco...@gm...>wrote: >>> >>> >>>> Hi all, >>>> >>>> Due to lots of things happening for all the OBI instrumenters, the >>>> recent calls were attended by Daniel, Frank and myself. >>>> >>>> Daniel has now left the EBI, Frank started working for a private >>>> company so won't have as much time as before to dedicate to OBI, and I >>>> won't be able to attend future instruments call either. >>>> >>>> We therefore propose to cancel those, unless other editors are willing >>>> to take on. >>>> >>>> Frank and myself had a chat during the OBI meeting last week: the >>>> instrument branch is in need of clean up, and in order to try and move >>>> forward with what we think would be the most efficient process we >>>> propose to try and coordinate via emails between the both of us. >>>> >>>> Obviously and for the reasons mentioned above this will be a slow >>>> process, so if you have any other suggestion or comment please let us >>>> know :) >>>> >>>> Melanie >>>> >>>> >>>> --- >>>> M?lanie Courtot >>>> TFL- BCCRC >>>> 675 West 10th Avenue >>>> Vancouver, BC >>>> V5Z 1L3, Canada >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Create and Deploy Rich Internet Apps outside the browser with >>>> Adobe(R)AIR(TM) >>>> software. With Adobe AIR, Ajax developers can use existing skills and >>>> code >>>> to >>>> build responsive, highly engaging applications that combine the power of >>>> local >>>> resources and data with the reach of the web. Download the Adobe AIR SDK >>>> and >>>> Ajax docs to start building applications today- >>>> http://p.sf.net/sfu/adobe-com >>>> _______________________________________________ >>>> Obi-instrument-branch mailing list >>>> Obi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Create and Deploy Rich Internet Apps outside the browser with >>> Adobe(R)AIR(TM) >>> software. With Adobe AIR, Ajax developers can use existing skills and code >>> to >>> build responsive, highly engaging applications that combine the power of >>> local >>> resources and data with the reach of the web. Download the Adobe AIR SDK >>> and >>> Ajax docs to start building applications today- >>> http://p.sf.net/sfu/adobe-com >>> _______________________________________________ >>> Obi-instrument-branch mailing list >>> Obi...@li... >>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>> >>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 10 Feb 2009 09:37:24 +0000 >> From: Frank Gibson <fg...@gm...> >> Subject: Re: [Obi-instrument-branch] instrument calls >> To: a.l...@ne... >> Cc: obi...@li... >> Message-ID: >> <65a...@ma...> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Hi, >> >> I think in this case, using collaborative protege may be overkill. I >> have used it before and I do think using collaborative protege should >> be the direction we should be heading in. However, in this case the >> editing required is minimal and is really just curating the terms with >> the new relations we have and fixing all the imported MSI terms, this >> can be handled offline with very little communication. >> >> For anyone that wants to edit the instrument branch the idea is to >> review everything under device, add missing funtions, has_supplier and >> device_setting and the other device relations and assert the classses >> under material entity rather than device. >> >> I will remove the instrument calls from the calendar unless anyone steps up >> >> Frank >> >> On Tue, Feb 10, 2009 at 9:08 AM, Allyson Lister >> <all...@go...> wrote: >> >>> Hi all, >>> >>> The idea of trying out collaborative protege sounds good. And, while I >>> don't >>> have much time for TCs right now, doing a little work here and there on >>> the >>> ontology might be something I can make time for, especially since the >>> instrument group is dropping in numbers. So, please include me on whatever >>> next steps you take! >>> >>> :) Allyson >>> >>> 2009/2/10 Trish Whetzel <plw...@gm...> >>> >>>> Since it sounds like you will need to intersperse conversations with >>>> changes to the owl file, would use of Collaborative Protege be helpful? >>>> >>>> Here are answers to questions brought up at the OBI workshop: >>>> 1) Can it do reasoning? >>>> Yes. >>>> >>>> 2) Can it save all versions? >>>> The edits are simultaneous in Collaborative Protege. There isn't really >>>> the concept of versions. Whatever change a user makes, all other users >>>> will >>>> see immediately. The ontology can be saved at any time in an OWL format >>>> and >>>> can be submitted to a SVN, if needed. >>>> >>>> 3) Can changes be rolled back? >>>> No. It is dangerous to do that with simultaneous editing. New version >>>> based on Protege 4 has that in plan. >>>> >>>> 4) Is the OWL file accessible in case there are special edits that need >>>> to >>>> be done offline that cannot be performed in Prot?g?? >>>> Yes. >>>> >>>> 5) Can the file be locked similar to a svn lock so that if offline work >>>> is >>>> needed, the file will be the same when added back to the server? >>>> No. Edits are simultaneous, so there are no versions. This "locking" >>>> feature is planned for the next version. >>>> >>>> 6) Is this an active project? >>>> Definitely. >>>> >>>> >>>> Trish >>>> >>>> >>>> On Mon, Feb 9, 2009 at 5:05 PM, Melanie Courtot <mco...@gm...> >>>> wrote: >>>> >>>>> Hi all, >>>>> >>>>> Due to lots of things happening for all the OBI instrumenters, the >>>>> recent calls were attended by Daniel, Frank and myself. >>>>> >>>>> Daniel has now left the EBI, Frank started working for a private >>>>> company so won't have as much time as before to dedicate to OBI, and I >>>>> won't be able to attend future instruments call either. >>>>> >>>>> We therefore propose to cancel those, unless other editors are willing >>>>> to take on. >>>>> >>>>> Frank and myself had a chat during the OBI meeting last week: the >>>>> instrument branch is in need of clean up, and in order to try and move >>>>> forward with what we think would be the most efficient process we >>>>> propose to try and coordinate via emails between the both of us. >>>>> >>>>> Obviously and for the reasons mentioned above this will be a slow >>>>> process, so if you have any other suggestion or comment please let us >>>>> know :) >>>>> >>>>> Melanie >>>>> >>>>> >>>>> --- >>>>> M?lanie Courtot >>>>> TFL- BCCRC >>>>> 675 West 10th Avenue >>>>> Vancouver, BC >>>>> V5Z 1L3, Canada >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Create and Deploy Rich Internet Apps outside the browser with >>>>> Adobe(R)AIR(TM) >>>>> software. With Adobe AIR, Ajax developers can use existing skills and >>>>> code to >>>>> build responsive, highly engaging applications that combine the power of >>>>> local >>>>> resources and data with the reach of the web. Download the Adobe AIR SDK >>>>> and >>>>> Ajax docs to start building applications >>>>> today-http://p.sf.net/sfu/adobe-com >>>>> _______________________________________________ >>>>> Obi-instrument-branch mailing list >>>>> Obi...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Create and Deploy Rich Internet Apps outside the browser with >>>> Adobe(R)AIR(TM) >>>> software. With Adobe AIR, Ajax developers can use existing skills and >>>> code >>>> to >>>> build responsive, highly engaging applications that combine the power of >>>> local >>>> resources and data with the reach of the web. Download the Adobe AIR SDK >>>> and >>>> Ajax docs to start building applications >>>> today-http://p.sf.net/sfu/adobe-com >>>> _______________________________________________ >>>> Obi-instrument-branch mailing list >>>> Obi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>>> >>>> >>> >>> -- >>> >>> Allyson Lister >>> http://lurena.vox.com >>> >>> CISBAN, http://www.cisban.ac.uk >>> Newcastle University >>> >>> >>> ------------------------------------------------------------------------------ >>> Create and Deploy Rich Internet Apps outside the browser with >>> Adobe(R)AIR(TM) >>> software. With Adobe AIR, Ajax developers can use existing skills and code >>> to >>> build responsive, highly engaging applications that combine the power of >>> local >>> resources and data with the reach of the web. Download the Adobe AIR SDK >>> and >>> Ajax docs to start building applications >>> today-http://p.sf.net/sfu/adobe-com >>> _______________________________________________ >>> Obi-instrument-branch mailing list >>> Obi...@li... >>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>> >>> >>> >> >> -- >> Frank Gibson, PhD >> http://peanutbutter.wordpress.com/ >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 11 Feb 2009 23:33:53 -0800 >> From: Trish Whetzel <plw...@gm...> >> Subject: Re: [Obi-instrument-branch] instrument calls >> To: Frank Gibson <fg...@gm...> >> Cc: obi...@li... >> Message-ID: >> <139...@ma...> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Got it, less discussions and decision-making, but more hands-on editing >> needed. >> >> Trish >> >> >> On Tue, Feb 10, 2009 at 1:37 AM, Frank Gibson <fg...@gm...> wrote: >> >> >>> Hi, >>> >>> I think in this case, using collaborative protege may be overkill. I >>> have used it before and I do think using collaborative protege should >>> be the direction we should be heading in. However, in this case the >>> editing required is minimal and is really just curating the terms with >>> the new relations we have and fixing all the imported MSI terms, this >>> can be handled offline with very little communication. >>> >>> For anyone that wants to edit the instrument branch the idea is to >>> review everything under device, add missing funtions, has_supplier and >>> device_setting and the other device relations and assert the classses >>> under material entity rather than device. >>> >>> I will remove the instrument calls from the calendar unless anyone steps >>> up >>> >>> Frank >>> >>> On Tue, Feb 10, 2009 at 9:08 AM, Allyson Lister >>> <all...@go...> wrote: >>> >>>> Hi all, >>>> >>>> The idea of trying out collaborative protege sounds good. And, while I >>>> >>> don't >>> >>>> have much time for TCs right now, doing a little work here and there on >>>> >>> the >>> >>>> ontology might be something I can make time for, especially since the >>>> instrument group is dropping in numbers. So, please include me on >>>> >>> whatever >>> >>>> next steps you take! >>>> >>>> :) Allyson >>>> >>>> 2009/2/10 Trish Whetzel <plw...@gm...> >>>> >>>>> Since it sounds like you will need to intersperse conversations with >>>>> changes to the owl file, would use of Collaborative Protege be helpful? >>>>> >>>>> Here are answers to questions brought up at the OBI workshop: >>>>> 1) Can it do reasoning? >>>>> Yes. >>>>> >>>>> 2) Can it save all versions? >>>>> The edits are simultaneous in Collaborative Protege. There isn't really >>>>> the concept of versions. Whatever change a user makes, all other users >>>>> >>> will >>> >>>>> see immediately. The ontology can be saved at any time in an OWL format >>>>> >>> and >>> >>>>> can be submitted to a SVN, if needed. >>>>> >>>>> 3) Can changes be rolled back? >>>>> No. It is dangerous to do that with simultaneous editing. New version >>>>> based on Protege 4 has that in plan. >>>>> >>>>> 4) Is the OWL file accessible in case there are special edits that need >>>>> >>> to >>> >>>>> be done offline that cannot be performed in Prot?g?? >>>>> Yes. >>>>> >>>>> 5) Can the file be locked similar to a svn lock so that if offline work >>>>> >>> is >>> >>>>> needed, the file will be the same when added back to the server? >>>>> No. Edits are simultaneous, so there are no versions. This "locking" >>>>> feature is planned for the next version. >>>>> >>>>> 6) Is this an active project? >>>>> Definitely. >>>>> >>>>> >>>>> Trish >>>>> >>>>> >>>>> On Mon, Feb 9, 2009 at 5:05 PM, Melanie Courtot <mco...@gm...> >>>>> wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> Due to lots of things happening for all the OBI instrumenters, the >>>>>> recent calls were attended by Daniel, Frank and myself. >>>>>> >>>>>> Daniel has now left the EBI, Frank started working for a private >>>>>> company so won't have as much time as before to dedicate to OBI, and I >>>>>> won't be able to attend future instruments call either. >>>>>> >>>>>> We therefore propose to cancel those, unless other editors are willing >>>>>> to take on. >>>>>> >>>>>> Frank and myself had a chat during the OBI meeting last week: the >>>>>> instrument branch is in need of clean up, and in order to try and move >>>>>> forward with what we think would be the most efficient process we >>>>>> propose to try and coordinate via emails between the both of us. >>>>>> >>>>>> Obviously and for the reasons mentioned above this will be a slow >>>>>> process, so if you have any other suggestion or comment please let us >>>>>> know :) >>>>>> >>>>>> Melanie >>>>>> >>>>>> >>>>>> --- >>>>>> M?lanie Courtot >>>>>> TFL- BCCRC >>>>>> 675 West 10th Avenue >>>>>> Vancouver, BC >>>>>> V5Z 1L3, Canada >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>> ------------------------------------------------------------------------------ >>> >>>>>> Create and Deploy Rich Internet Apps outside the browser with >>>>>> Adobe(R)AIR(TM) >>>>>> software. With Adobe AIR, Ajax developers can use existing skills and >>>>>> code to >>>>>> build responsive, highly engaging applications that combine the power >>>>>> >>> of >>> >>>>>> local >>>>>> resources and data with the reach of the web. Download the Adobe AIR >>>>>> >>> SDK >>> >>>>>> and >>>>>> Ajax docs to start building applications >>>>>> today-http://p.sf.net/sfu/adobe-com >>>>>> _______________________________________________ >>>>>> Obi-instrument-branch mailing list >>>>>> Obi...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>>>>> >>>>> >>>>> >>>>> >>> ------------------------------------------------------------------------------ >>> >>>>> Create and Deploy Rich Internet Apps outside the browser with >>>>> Adobe(R)AIR(TM) >>>>> software. With Adobe AIR, Ajax developers can use existing skills and >>>>> >>> code >>> >>>>> to >>>>> build responsive, highly engaging applications that combine the power >>>>> of >>>>> local >>>>> resources and data with the reach of the web. Download the Adobe AIR >>>>> SDK >>>>> and >>>>> Ajax docs to start building applications >>>>> today-http://p.sf.net/sfu/adobe-com >>>>> _______________________________________________ >>>>> Obi-instrument-branch mailing list >>>>> Obi...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>>>> >>>>> >>>> >>>> -- >>>> >>>> Allyson Lister >>>> http://lurena.vox.com >>>> >>>> CISBAN, http://www.cisban.ac.uk >>>> Newcastle University >>>> >>>> >>>> >>> ------------------------------------------------------------------------------ >>> >>>> Create and Deploy Rich Internet Apps outside the browser with >>>> Adobe(R)AIR(TM) >>>> software. With Adobe AIR, Ajax developers can use existing skills and >>>> >>> code >>> >>>> to >>>> build responsive, highly engaging applications that combine the power of >>>> local >>>> resources and data with the reach of the web. Download the Adobe AIR SDK >>>> >>> and >>> >>>> Ajax docs to start building applications today- >>>> >>> http://p.sf.net/sfu/adobe-com >>> >>>> _______________________________________________ >>>> Obi-instrument-branch mailing list >>>> Obi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >>>> >>>> >>>> >>> >>> -- >>> Frank Gibson, PhD >>> http://peanutbutter.wordpress.com/ >>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> Create and Deploy Rich Internet Apps outside the browser with >> Adobe(R)AIR(TM) >> software. With Adobe AIR, Ajax developers can use existing skills and code >> to >> build responsive, highly engaging applications that combine the power of >> local >> resources and data with the reach of the web. Download the Adobe AIR SDK and >> Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com >> >> ------------------------------ >> >> _______________________________________________ >> Obi-instrument-branch mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >> >> >> End of Obi-instrument-branch Digest, Vol 25, Issue 2 >> **************************************************** >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> ------------------------------------------------------------------------------ >> Create and Deploy Rich Internet Apps outside the browser with >> Adobe(R)AIR(TM) >> software. With Adobe AIR, Ajax developers can use existing skills and code >> to >> build responsive, highly engaging applications that combine the power of >> local >> resources and data with the reach of the web. Download the Adobe AIR SDK and >> Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com >> _______________________________________________ >> Obi-instrument-branch mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >> >> >> > > > > |