From Serguei.Krivov at uvm.edu Wed Feb 16 09:12:29 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Wed, 16 Feb 2005 12:12:29 -0500 Subject: [seek-kr-sms] a presentation on data integration Message-ID: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> Here is a 2005 presentation on data integration from Slovak Republic- http://www.sofsem.sk/presentations/sofsem05-lenzerini.pdf Seems it is very close to Shawns & Bertrams work, save it is based more on FOL serguei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20050216/f94d00c7/attachment.htm From ludaesch at ucdavis.edu Wed Feb 16 09:26:20 2005 From: ludaesch at ucdavis.edu (Bertram Ludaescher) Date: Wed, 16 Feb 2005 09:26:20 -0800 Subject: [seek-kr-sms] a presentation on data integration In-Reply-To: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> References: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> Message-ID: <16915.33340.807000.500596@gargle.gargle.HOWL> Thanks Serguei for the pointer! Actually other stuff is also based on FO, but we hide it better ;-) Bertram Serguei Krivov writes: > Here is a 2005 presentation on data integration from Slovak Republic- > http://www.sofsem.sk/presentations/sofsem05-lenzerini.pdf > Seems it is very close to Shawns & Bertrams work, save it is based more > on FOL > > serguei > > > > > > > > > > > > > > name="PlaceName"/> > name="PlaceType"/> > name="place"/> > > > > > > > >

> >

Here is a 2005 presentation on data integration from size=2 face=Arial>Slovak size=2 face=Arial> size=2 face=Arial>Republic- size=2 face=Arial>

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href="http://www.sofsem.sk/presentations/sofsem05-lenzerini.pdf">http://www.sofsem.sk/presentations/sofsem05-lenzerini.pdf

> >

Seems it is very close to Shawns > & Bertrams work, save it is based more on FOL

> >

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> >

> > > > From goguen at cs.ucsd.edu Wed Feb 16 09:27:34 2005 From: goguen at cs.ucsd.edu (Joseph Goguen) Date: Wed, 16 Feb 2005 09:27:34 -0800 Subject: [seek-kr-sms] a presentation on data integration In-Reply-To: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> References: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> Message-ID: <42138286.2030604@cs.ucsd.edu> Actually this is from Rome, where Lenzerini is professor of information systems; his work is excellent, and he is a very nice guy. I spent a week with him this summer, and lectured on our schema mapping work to his group. He wants to try our SCIA system and is excited by our work on abstract schema morphisms; he also liked our critical point interaction ideas and wants to implement it also. (SEEK supported my "ontological tour" of Italy.) -- joseph Serguei Krivov wrote: > Here is a 2005 presentation on data integration from Slovak Republic- > > http://www.sofsem.sk/presentations/sofsem05-lenzerini.pdf > > Seems it is very close to Shawns & Bertrams work, save it is based > more on FOL > > > > serguei > > > > > > > From ludaesch at ucdavis.edu Wed Feb 16 09:31:30 2005 From: ludaesch at ucdavis.edu (Bertram Ludaescher) Date: Wed, 16 Feb 2005 09:31:30 -0800 Subject: [seek-kr-sms] a presentation on data integration In-Reply-To: <42138286.2030604@cs.ucsd.edu> References: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> <42138286.2030604@cs.ucsd.edu> Message-ID: <16915.33650.642000.427700@gargle.gargle.HOWL> Thanks Joseph -- This is great! It is important for SEEK to have these strong links with the core CS community (in addition to the ongoing tools development). cheers Bertram Joseph Goguen writes: > Actually this is from Rome, where Lenzerini is professor of information > systems; > his work is excellent, and he is a very nice guy. I spent a week with > him this summer, > and lectured on our schema mapping work to his group. He wants to try > our SCIA > system and is excited by our work on abstract schema morphisms; he also > liked our > critical point interaction ideas and wants to implement it also. (SEEK > supported my > "ontological tour" of Italy.) > > -- joseph > > Serguei Krivov wrote: > > > Here is a 2005 presentation on data integration from Slovak Republic- > > > > http://www.sofsem.sk/presentations/sofsem05-lenzerini.pdf > > > > Seems it is very close to Shawns & Bertrams work, save it is based > > more on FOL > > > > > > > > serguei > > > > > > > > > > > > > > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From jones at nceas.ucsb.edu Tue Feb 22 10:56:58 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Tue, 22 Feb 2005 09:56:58 -0900 Subject: [seek-kr-sms] [Fwd: [Fwd: Ecoterm environmental terminology mtg]] Message-ID: <421B807A.7010809@nceas.ucsb.edu> Forwarding again, got the seek-kr-sms address wrong last time. Oops. Matt -------------- next part -------------- An embedded message was scrubbed... From: Matt Jones Subject: [Fwd: Ecoterm environmental terminology mtg] Date: Mon, 21 Feb 2005 09:45:09 -0900 Size: 9282 Url: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20050222/34da3de2/Ecotermenvironmentalterminologymtg.eml From jones at nceas.ucsb.edu Tue Feb 22 10:57:53 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Tue, 22 Feb 2005 09:57:53 -0900 Subject: [seek-kr-sms] [Fwd: [Fwd: Re: Measurement scale in EML]] Message-ID: <421B80B1.9090807@nceas.ucsb.edu> And another forward that I messed up... Matt -------------- next part -------------- An embedded message was scrubbed... From: Matt Jones Subject: [Fwd: Re: Measurement scale in EML] Date: Mon, 21 Feb 2005 09:51:17 -0900 Size: 20196 Url: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20050222/feb0fed8/MeasurementscaleinEML.eml From peter.mccartney at asu.edu Tue Feb 22 14:21:09 2005 From: peter.mccartney at asu.edu (Peter McCartney) Date: Tue, 22 Feb 2005 15:21:09 -0700 Subject: [seek-kr-sms] [Fwd: [Fwd: Ecoterm environmental terminology mtg]] In-Reply-To: <421B807A.7010809@nceas.ucsb.edu> References: <421B807A.7010809@nceas.ucsb.edu> Message-ID: <1109110869.5622.9.camel@phmlaptop> their website seems to inidicat a lot of activities that overlap with our community, although its hard to tell how mature many of them are. the immediate workshop topic is directly relevant and timely though. i think someone should go. On Tue, 2005-02-22 at 09:56 -0900, Matt Jones wrote: > Forwarding again, got the seek-kr-sms address wrong last time. Oops. > > Matt > > email message attachment ([Fwd: Ecoterm environmental terminology > mtg]) > On Tue, 2005-02-22 at 09:56 -0900, Matt Jones wrote: > > Hi Mark, > > > > This meeting seemed relevant to the KR and maybe SMS groups. Gail > > Hodges used to be involved in the Ceres/NBII thesaurus project, and now > > appears to be in the EU. I also hadn't seen this Ecoinformatics > > Initiative web site before. Interesting. Do you think we should send > > anyone over that has knowledge of our ontologies? > > > > Matt > > > > > > email message attachment (INVITATION: 2nd ECOTERM MEETING ON > > ADVANCING ENVIRONMENTAL TERMINOLOGY) > > On Tue, 2005-02-22 at 09:56 -0900, Matt Jones wrote: > > > SOME OF YOU RECEIVED AN INVITATION TO A MORE LIMITED VERSION OF > > > THIS MEETING LAST YEAR IN GENEVA BUT WEREN'T ABLE TO ATTEND. WE > > > HOPE THAT YOU WILL BE ABLE TO JOIN US THIS YEAR. NEW GROUP MEMBERS > > > ARE ALWAYS WELCOME. > > > > > > PLEASE FEEL FREE TO DISTRIBUTE TO OTHERS WHO MIGHT BE INTERESTED. > > > THIS IS BEING DISTRIBUTED TO SEVERAL LISTS. APOLOGIES IN ADVANCE > > > FOR DUPLICATION. > > > > > > ANNOUNCING THE 2ND ECOTERM MEETING > > > The German Federal Environment Agency > > > (UBA- Umweltbundesamt) > > > Offices 1, Berlin Grunewald > > > Bismarckplatz 1, > > > Berlin, Germany > > > 15 April 2005 > > > > > > > > > In April 2004 the Ecoterm Group was formed by parties interested > > > in working together on environmental terminologies, their > > > integration and their use with semantic web technologies. The > > > Ecoterm Group is a working group of the Ecoinformatics Initiative > > > (http://ecoinfo.eionet.eu.int/ ). > > > > > > The second meeting of the Ecoterm Group will take place at the UBA > > > in Berlin on 15 April 2005. > > > > > > The agenda will include an update on the activities that resulted > > > from the Ecoterm Meeting in Geneva in April 2004, updates on > > > individual projects from the participants, and an update on > > > progress in relevant standards and tool development. A formal > > > agenda is still being prepared. > > > > > > There is no registration cost. Meals will be on your own. > > > > > > Please register at http://ecoterm.infointl.com > > > Note that this registration form will not register you for the > > > OpenForum. (See the OpenForum information below.) > > > > > > You can find information about the location of UBA at: > > > http://www.umweltdaten.de/down-e/anreise.pdf > > > > > > > > > >From Crowne Plaza, the location for the OpenForum, you can reach > > > UBA within 20 minutes with Bus X10. The following hotels are very > > > close to UBA (within 10 minutes of walking distance) should you > > > choose to be closer to the location for the Ecoterm Meeting: > > > http://www.kronprinz-hotel.de/ > > > > > > and > > > http://www.hotel-haus-bismarck.de/index.html > > > > > > > > > The meeting will take place the day after the Open Forum on > > > Metadata Registries, which will include a significant number of > > > terminology related presentations. We encourage you to come early > > > and attend the Open Forum. The topic, "Semantic Interoperability: > > > Where Meaning Meets Metadata" will be very relevant to our > > > discussions on Friday. Information about the Open Forum, > > > including hotel reservations, can be found at > > > http://www.berlinopenforum.de/. Note that the OpenForum > > > registration form will not register you for the Ecoterm Meeting. > > > (See the registration information above.) We encourage you to come > > > early and attend the OpenForum. > > > > > > We look forward to seeing you in Berlin. > > > > > > Gail Hodge > > > Ecoterm Meeting Organizer > > > > > > Sr. Information Scientist > > > Consultant to the US Geological Survey > > > Information International Associates, Inc. > > > 312 Walnut Place > > > Havertown, Pennsylvania 19083 USA > > > +1 865-742-5430 (cell) > > > +1 865-481-0390 (fax) > > > gailhodge at aol.com > > > > > > > > > > > > From Serguei.Krivov at uvm.edu Wed Feb 23 11:39:52 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Wed, 23 Feb 2005 14:39:52 -0500 Subject: [seek-kr-sms] GrOWL/Jena Message-ID: <000001c519df$7193a4f0$3ca6c684@BTS2K3000D5635086B> The first version of GrOWL based entirely on Jena is in CVS. I also implemented layout style sheets. Now static layout is default for GrOWL. It uses layout engine only when layout style sheet is not available. serguei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20050223/e20e4ff8/attachment.htm From Serguei.Krivov at uvm.edu Wed Feb 23 13:01:00 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Wed, 23 Feb 2005 16:01:00 -0500 Subject: [seek-kr-sms] GrOWL/Jena In-Reply-To: <421CE35F.9050000@ucdavis.edu> Message-ID: <000201c519ea$c71b6470$3ca6c684@BTS2K3000D5635086B> Hi Shawn, In fact by layout style sheet I meant a simple thing - an xml files that stores x, y coordinates for each node. When ontology file say camera.owl, is loaded, growl will also look for another file- camera.owl.layout. If it is found then the information from that file is used to restore the old position of nodes. Thus , if ontology map was positioned once - it could be restored with exactly same shape and TG auto-layout thing becomes unnecessary. Automatic layout still works and perhaps I should find some way to lock it, so that it is not activated by mistake. As you see the layout style sheet is just exactly what you asked us to implement sometime ago and as I understand it - the whole idea of layout style sheet was yours. Cheers, serguei This is great! The style sheets sound interesting. Can you give some examples of how the layout style sheets would be used? What can one do with them, and what kind of "looks" can be created? Thanks, Shawn Serguei Krivov wrote: > The first version of GrOWL based entirely on Jena is in CVS. I also > implemented layout style sheets. Now static layout is default for GrOWL. > It uses layout engine only when layout style sheet is not available. > > > > serguei > > > > > > > > > From Manu.Juyal at asu.edu Thu Feb 24 15:05:42 2005 From: Manu.Juyal at asu.edu (Manu Juyal) Date: Thu, 24 Feb 2005 16:05:42 -0700 (MST) Subject: [seek-kr-sms] Ontology (Rich) links found broken Message-ID: <1109286342.421e5dc656a87@webmail.asu.edu> Hi All, I am working on ontology-based detection of disharmony between different dataset and generation of necessary workflow for subsequent reconciliation. I was extending a part of the ontologies that Rich was working on. They were working fine till last night but this morning I figured out that links to those ontologies are broken. Can anyone give me any clue about possible alternative for accessing those ontologies. -Manu From berkley at nceas.ucsb.edu Thu Feb 24 15:10:55 2005 From: berkley at nceas.ucsb.edu (Chad Berkley) Date: Thu, 24 Feb 2005 15:10:55 -0800 Subject: [seek-kr-sms] Ontology (Rich) links found broken In-Reply-To: <1109286342.421e5dc656a87@webmail.asu.edu> References: <1109286342.421e5dc656a87@webmail.asu.edu> Message-ID: <421E5EFF.3010202@nceas.ucsb.edu> You can get them from CVS. Check here: http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/seek/projects/kr-sms/ chad Manu Juyal wrote: > Hi All, > I am working on ontology-based detection of disharmony between different > dataset and generation of necessary workflow for subsequent reconciliation. > > I was extending a part of the ontologies that Rich was working on. They were > working fine till last night but this morning I figured out that links to > those ontologies are broken. Can anyone give me any clue about possible > alternative for accessing those ontologies. > > -Manu > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From Manu.Juyal at asu.edu Thu Feb 24 15:19:48 2005 From: Manu.Juyal at asu.edu (Manu Juyal) Date: Thu, 24 Feb 2005 16:19:48 -0700 (MST) Subject: [seek-kr-sms] Ontology (Rich) links found broken Message-ID: <1109287188.421e61148ed31@webmail.asu.edu> I tried them but they are not working either because they themselves are refering to many other ontologies at http://wow.sfsu.edu/ontology/rich From jones at nceas.ucsb.edu Thu Feb 24 15:30:31 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Thu, 24 Feb 2005 14:30:31 -0900 Subject: [seek-kr-sms] Ontology (Rich) links found broken In-Reply-To: <1109287188.421e61148ed31@webmail.asu.edu> References: <1109287188.421e61148ed31@webmail.asu.edu> Message-ID: <421E6397.207@nceas.ucsb.edu> Yeah, Rich addressed this before I think. I think the key is downloading local copies (ie, cvs checkout) which you register with your local ontology editor (e.g., protoge) so that it knows it has a version of the ontology for a given namespace. In other words, you can override the ontology file locations based on namespace by configuring your editor properly. This is a standard problem with external pointers that is solved best by this extra level of indirection. Rich posted about this earlier to the SEEK group. Matt Manu Juyal wrote: > I tried them but they are not working either because they themselves are > refering to many other ontologies at http://wow.sfsu.edu/ontology/rich > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- From rwilliams at nceas.ucsb.edu Thu Feb 24 19:58:10 2005 From: rwilliams at nceas.ucsb.edu (Rich Williams) Date: Thu, 24 Feb 2005 19:58:10 -0800 Subject: [seek-kr-sms] Ontology (Rich) links found broken In-Reply-To: <421E6397.207@nceas.ucsb.edu> Message-ID: You got it. The method for doing this in Jena involves defining alternate ontology locations in file called ont-policy.rdf. Protege uses this mechanism, since it uses the Jena libraries. And if you're writing code that uses Jena, I'd recommend having it use the same mechanism. Rich > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org]On Behalf Of Matt Jones > Sent: Thursday, February 24, 2005 3:31 PM > To: Manu Juyal > Cc: seek-kr-sms at ecoinformatics.org > Subject: Re: [seek-kr-sms] Ontology (Rich) links found broken > > > Yeah, Rich addressed this before I think. I think the key is > downloading local copies (ie, cvs checkout) which you register with your > local ontology editor (e.g., protoge) so that it knows it has a version > of the ontology for a given namespace. In other words, you can override > the ontology file locations based on namespace by configuring your > editor properly. This is a standard problem with external pointers that > is solved best by this extra level of indirection. Rich posted about > this earlier to the SEEK group. > > Matt > > Manu Juyal wrote: > > I tried them but they are not working either because they > themselves are > > refering to many other ontologies at http://wow.sfsu.edu/ontology/rich > > _______________________________________________ > > seek-kr-sms mailing list > > seek-kr-sms at ecoinformatics.org > > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > -- > ------------------------------------------------------------------- > Matt Jones jones at nceas.ucsb.edu > http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 > National Center for Ecological Analysis and Synthesis (NCEAS) > University of California Santa Barbara > Interested in ecological informatics? http://www.ecoinformatics.org > ------------------------------------------------------------------- > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From jones at nceas.ucsb.edu Fri Feb 25 13:00:14 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Fri, 25 Feb 2005 12:00:14 -0900 Subject: [seek-kr-sms] running growl from CVS Message-ID: <421F91DE.4010608@nceas.ucsb.edu> Sergui, I'm trying to look at the new growl from CVS. We'd like to evaluate how it might be used in Kepler for ontology UI stuff. Unfortunately, here's no readme, docs, ant build file (build.xml), makefile, batch file, or shell script that's relevant as far as I can tell in the ontobrowser directory. Can you help me out? 1) Is the source in "seek/projects/kr-sms/ontobrowser" ? 2) How do I build Growl from source? 3) How do I run Growl once built? Thanks. Matt -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- From Serguei.Krivov at uvm.edu Fri Feb 25 13:50:56 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Fri, 25 Feb 2005 16:50:56 -0500 Subject: [seek-kr-sms] running growl from CVS In-Reply-To: <421F91DE.4010608@nceas.ucsb.edu> Message-ID: <000301c51b84$1619a6a0$3ca6c684@BTS2K3000D5635086B> Hi Matt, Sorry for the mess with the code and docs. We intended to clean it before the beta release. At this point we are still in the stage of alpha. Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as a consequence we did not use any separate utility for building project. If you do not use eclipse or NB then we have to think how to port GrOWL to your type of project. My impression however was that most of us who do java use eclipse. If you have eclipse then compiling with GrOWL/Jena is easy (comparing to compiling GrOWL?OWLAPI): 1. Install Jena, or have (ALL)Jena jars ready 2.If you are using eclipse CVS check out directory kr-sms/ontobrowser/src: right click on it, select Check Out As, select Java Project and go through the steps that the wizards offer. Assume that the project name you selected is "ontobrowser" If using external CVS , get the code and create new project e.g. "ontobrowser" using directory kr-sms/ontobrowser/src as top directory of the project. 3. Project will be compiled with many errors. Get to the "property dialog "of the project "ontobrowser" (for this one can right click on the project, select "properties" from the bottom of popup menu, or select the project in the explorer and then go to Menu: Project | Properties) In the property dialog click on Java Build Path (on the left). Then select pane Libraries, then click button AddExternal Jars and add ALL jena jars to the project. After this project should compile. There will be still errors in the code related to OWLAPI part, and in the old code, but these are negligible. 4. To execute: in package explorer select org/ecoinformatics/seek/growl/editor/GrowlEditor.java then in menu Run select: Run As | Java Application If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for code, Add the same external jars of Jena. Please let me know if more detailed description could be more useful. At the moment browsing of large ontologies is not really great. I am working on graphic filters that would allow to select a class and view separately a)its definition, b)its instances, c) references to this class etc . After this is done (by next week) browsing of large ontologies will be easy. serguei -----Original Message----- From: seek-kr-sms-admin at ecoinformatics.org [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones Sent: Friday, February 25, 2005 4:00 PM To: Sergui Krivov Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org Subject: [seek-kr-sms] running growl from CVS Sergui, I'm trying to look at the new growl from CVS. We'd like to evaluate how it might be used in Kepler for ontology UI stuff. Unfortunately, here's no readme, docs, ant build file (build.xml), makefile, batch file, or shell script that's relevant as far as I can tell in the ontobrowser directory. Can you help me out? 1) Is the source in "seek/projects/kr-sms/ontobrowser" ? 2) How do I build Growl from source? 3) How do I run Growl once built? Thanks. Matt -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- _______________________________________________ seek-kr-sms mailing list seek-kr-sms at ecoinformatics.org http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From sbowers at ucdavis.edu Fri Feb 25 13:58:30 2005 From: sbowers at ucdavis.edu (Shawn Bowers) Date: Fri, 25 Feb 2005 13:58:30 -0800 Subject: [seek-kr-sms] running growl from CVS In-Reply-To: <000301c51b84$1619a6a0$3ca6c684@BTS2K3000D5635086B> References: <000301c51b84$1619a6a0$3ca6c684@BTS2K3000D5635086B> Message-ID: <421F9F86.2020600@ucdavis.edu> For those of us who like to do it the old-fashioned way; perhaps you could stick a new GrowlEditor.jar file somewhere (e.g., in cvs) that we could just run without having to compile, etc. thanks, shawn Serguei Krivov wrote: > Hi Matt, > Sorry for the mess with the code and docs. We intended to clean it > before the beta release. At this point we are still in the stage of > alpha. > > Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as a > consequence we did not use any separate utility for building project. If > you do not use eclipse or NB then we have to think how to port GrOWL to > your type of project. My impression however was that most of us who do > java use eclipse. > > If you have eclipse then compiling with GrOWL/Jena is easy (comparing to > compiling GrOWL?OWLAPI): > 1. Install Jena, or have (ALL)Jena jars ready > 2.If you are using eclipse CVS check out directory > kr-sms/ontobrowser/src: > right click on it, select Check Out As, select Java Project and go > through the steps that the wizards offer. Assume that the project name > you selected is "ontobrowser" > If using external CVS , get the code and create new project e.g. > "ontobrowser" using directory kr-sms/ontobrowser/src as top directory of > the project. > > 3. Project will be compiled with many errors. Get to the "property > dialog "of the project "ontobrowser" (for this one can right click on > the project, select "properties" from the bottom of popup menu, or > select the project in the explorer and then go to Menu: Project | > Properties) > In the property dialog click on Java Build Path (on the left). Then > select pane Libraries, then click button AddExternal Jars and add ALL > jena jars to the project. > After this project should compile. There will be still errors in the > code related to OWLAPI part, and in the old code, but these are > negligible. > > 4. To execute: in package explorer select > org/ecoinformatics/seek/growl/editor/GrowlEditor.java > then in menu Run select: Run As | Java Application > > > If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for > code, > Add the same external jars of Jena. > > Please let me know if more detailed description could be more useful. > > At the moment browsing of large ontologies is not really great. I am > working on graphic filters that would allow to select a class and view > separately a)its definition, b)its instances, c) references to this > class etc . After this is done (by next week) browsing of large > ontologies will be easy. > > > serguei > > > > > > > > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones > Sent: Friday, February 25, 2005 4:00 PM > To: Sergui Krivov > Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org > Subject: [seek-kr-sms] running growl from CVS > > Sergui, > > I'm trying to look at the new growl from CVS. We'd like to evaluate how > > it might be used in Kepler for ontology UI stuff. Unfortunately, > here's no readme, docs, ant build file (build.xml), makefile, batch > file, or shell script that's relevant as far as I can tell in the > ontobrowser directory. Can you help me out? > > 1) Is the source in "seek/projects/kr-sms/ontobrowser" ? > 2) How do I build Growl from source? > 3) How do I run Growl once built? > > Thanks. > > Matt > From ferdinando.villa at uvm.edu Fri Feb 25 14:00:24 2005 From: ferdinando.villa at uvm.edu (Ferdinando Villa) Date: Fri, 25 Feb 2005 17:00:24 -0500 Subject: [seek-kr-sms] running growl from CVS In-Reply-To: <421F9F86.2020600@ucdavis.edu> Message-ID: <000001c51b85$68b09350$2aa6c684@ECOINFORMATICS> I think an Ant build file could peacefully coexist with the Eclipse project and wouldn't be so hard to set up, right? And yes, I also think executable jars (at least for the editor) should be in cvs. ferdinando -----Original Message----- From: seek-kr-sms-admin at ecoinformatics.org [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Shawn Bowers Sent: Friday, February 25, 2005 4:59 PM To: Serguei Krivov Cc: seek-kr-sms at ecoinformatics.org Subject: Re: [seek-kr-sms] running growl from CVS For those of us who like to do it the old-fashioned way; perhaps you could stick a new GrowlEditor.jar file somewhere (e.g., in cvs) that we could just run without having to compile, etc. thanks, shawn Serguei Krivov wrote: > Hi Matt, > Sorry for the mess with the code and docs. We intended to clean it > before the beta release. At this point we are still in the stage of > alpha. > > Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as > a consequence we did not use any separate utility for building > project. If you do not use eclipse or NB then we have to think how to > port GrOWL to your type of project. My impression however was that > most of us who do java use eclipse. > > If you have eclipse then compiling with GrOWL/Jena is easy (comparing > to compiling GrOWL?OWLAPI): 1. Install Jena, or have (ALL)Jena jars > ready 2.If you are using eclipse CVS check out directory > kr-sms/ontobrowser/src: > right click on it, select Check Out As, select Java Project and go > through the steps that the wizards offer. Assume that the project name > you selected is "ontobrowser" > If using external CVS , get the code and create new project e.g. > "ontobrowser" using directory kr-sms/ontobrowser/src as top directory of > the project. > > 3. Project will be compiled with many errors. Get to the "property > dialog "of the project "ontobrowser" (for this one can right click on > the project, select "properties" from the bottom of popup menu, or > select the project in the explorer and then go to Menu: Project | > Properties) > In the property dialog click on Java Build Path (on the left). Then > select pane Libraries, then click button AddExternal Jars and add ALL > jena jars to the project. After this project should compile. There > will be still errors in the code related to OWLAPI part, and in the > old code, but these are negligible. > > 4. To execute: in package explorer select > org/ecoinformatics/seek/growl/editor/GrowlEditor.java > then in menu Run select: Run As | Java Application > > > If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for > code, Add the same external jars of Jena. > > Please let me know if more detailed description could be more useful. > > At the moment browsing of large ontologies is not really great. I am > working on graphic filters that would allow to select a class and > view separately a)its definition, b)its instances, c) references to > this class etc . After this is done (by next week) browsing of large > ontologies will be easy. > > > serguei > > > > > > > > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones > Sent: Friday, February 25, 2005 4:00 PM > To: Sergui Krivov > Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org > Subject: [seek-kr-sms] running growl from CVS > > Sergui, > > I'm trying to look at the new growl from CVS. We'd like to evaluate > how > > it might be used in Kepler for ontology UI stuff. Unfortunately, > here's no readme, docs, ant build file (build.xml), makefile, batch > file, or shell script that's relevant as far as I can tell in the > ontobrowser directory. Can you help me out? > > 1) Is the source in "seek/projects/kr-sms/ontobrowser" ? > 2) How do I build Growl from source? > 3) How do I run Growl once built? > > Thanks. > > Matt > _______________________________________________ seek-kr-sms mailing list seek-kr-sms at ecoinformatics.org http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From jones at nceas.ucsb.edu Fri Feb 25 16:43:15 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Fri, 25 Feb 2005 15:43:15 -0900 Subject: [seek-kr-sms] ontology/folder UI design in Kepler Message-ID: <421FC623.7040509@nceas.ucsb.edu> Messed up the list address ... sending again... sorry for the duplicate laura. Matt -------- Original message ------------------ Hi Laura, Chad, Shawn, and I have been discussing the tree control on the left side of the Kepler window. Chad and Shawn are currently modifying it to allow creation of new nodes in the ontology. In doing so, we've recognized a bunch of problems with using the informal 'folder' concept to represent an ontology class. The Growl editor is a more acurate representation of the ontology but has limitations given the small space we are trying to use in Kepler to discuss this stuff. We need to resolve this to make the UI clear and not have the users mess up the ontology as they add new concepts and actors. The attached log of our IRC conversation describes some of the issues. Could you review it, and then we can discuss how to reach our goal. I think its important to have you involved at this design stage. Chad and Shawn are implementing now so we need to provide feedback asap. Maybe we can have a conference call next week? Thanks. Matt -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ontology-ui-#seek-discussion-20050225.txt Url: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20050225/0528ed13/ontology-ui-seek-discussion-20050225.txt From Serguei.Krivov at uvm.edu Fri Feb 25 16:55:16 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Fri, 25 Feb 2005 19:55:16 -0500 Subject: [seek-kr-sms] running growl from CVS In-Reply-To: <000001c51b85$68b09350$2aa6c684@ECOINFORMATICS> Message-ID: <000001c51b9d$d61b5ca0$3ca6c684@BTS2K3000D5635086B> OK I shall create jar as soon as I get stable version with graphic filters. I will be refreshing jar with each stable buld. Maintaining Ant file on the other hand is about as easy and pleasurable as manual maintaining of configure file for a large C++ project. One tends to always forget adding newly created *.h and *.cc files to configure ( so I always wanted to use IDEs as KDeveloper or Anjuta that relieve me from maintaining configure files ). Thanks to Eclipse and Netbeans Ant became completely unnecessary for java developers, users and testers on the other hand normally do not need to recompile java code for their specific platform, so neither they need a tool ala "configure" if jar is provided. Having said so, I will create Ant file for GrOWL if there is at least one developer who would make use of it or if there is at least one tester who would prefer Ant file to jar. Please let me know... serguei ------------------------------------------------------------------------ -------------- Serguei Krivov, Assist. Research Professor, Computer Science Dept. & Gund Inst. for Ecological Economics, University of Vermont; 590 Main St. Burlington VT 05405 phone: (802)-656-2978 -----Original Message----- From: seek-kr-sms-admin at ecoinformatics.org [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Ferdinando Villa Sent: Friday, February 25, 2005 5:00 PM To: 'Shawn Bowers'; 'Serguei Krivov' Cc: seek-kr-sms at ecoinformatics.org Subject: RE: [seek-kr-sms] running growl from CVS I think an Ant build file could peacefully coexist with the Eclipse project and wouldn't be so hard to set up, right? And yes, I also think executable jars (at least for the editor) should be in cvs. ferdinando -----Original Message----- From: seek-kr-sms-admin at ecoinformatics.org [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Shawn Bowers Sent: Friday, February 25, 2005 4:59 PM To: Serguei Krivov Cc: seek-kr-sms at ecoinformatics.org Subject: Re: [seek-kr-sms] running growl from CVS For those of us who like to do it the old-fashioned way; perhaps you could stick a new GrowlEditor.jar file somewhere (e.g., in cvs) that we could just run without having to compile, etc. thanks, shawn Serguei Krivov wrote: > Hi Matt, > Sorry for the mess with the code and docs. We intended to clean it > before the beta release. At this point we are still in the stage of > alpha. > > Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as > a consequence we did not use any separate utility for building > project. If you do not use eclipse or NB then we have to think how to > port GrOWL to your type of project. My impression however was that > most of us who do java use eclipse. > > If you have eclipse then compiling with GrOWL/Jena is easy (comparing > to compiling GrOWL?OWLAPI): 1. Install Jena, or have (ALL)Jena jars > ready 2.If you are using eclipse CVS check out directory > kr-sms/ontobrowser/src: > right click on it, select Check Out As, select Java Project and go > through the steps that the wizards offer. Assume that the project name > you selected is "ontobrowser" > If using external CVS , get the code and create new project e.g. > "ontobrowser" using directory kr-sms/ontobrowser/src as top directory of > the project. > > 3. Project will be compiled with many errors. Get to the "property > dialog "of the project "ontobrowser" (for this one can right click on > the project, select "properties" from the bottom of popup menu, or > select the project in the explorer and then go to Menu: Project | > Properties) > In the property dialog click on Java Build Path (on the left). Then > select pane Libraries, then click button AddExternal Jars and add ALL > jena jars to the project. After this project should compile. There > will be still errors in the code related to OWLAPI part, and in the > old code, but these are negligible. > > 4. To execute: in package explorer select > org/ecoinformatics/seek/growl/editor/GrowlEditor.java > then in menu Run select: Run As | Java Application > > > If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for > code, Add the same external jars of Jena. > > Please let me know if more detailed description could be more useful. > > At the moment browsing of large ontologies is not really great. I am > working on graphic filters that would allow to select a class and > view separately a)its definition, b)its instances, c) references to > this class etc . After this is done (by next week) browsing of large > ontologies will be easy. > > > serguei > > > > > > > > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones > Sent: Friday, February 25, 2005 4:00 PM > To: Sergui Krivov > Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org > Subject: [seek-kr-sms] running growl from CVS > > Sergui, > > I'm trying to look at the new growl from CVS. We'd like to evaluate > how > > it might be used in Kepler for ontology UI stuff. Unfortunately, > here's no readme, docs, ant build file (build.xml), makefile, batch > file, or shell script that's relevant as far as I can tell in the > ontobrowser directory. Can you help me out? > > 1) Is the source in "seek/projects/kr-sms/ontobrowser" ? > 2) How do I build Growl from source? > 3) How do I run Growl once built? > > Thanks. > > Matt > _______________________________________________ seek-kr-sms mailing list seek-kr-sms at ecoinformatics.org http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms _______________________________________________ seek-kr-sms mailing list seek-kr-sms at ecoinformatics.org http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From Serguei.Krivov at uvm.edu Fri Feb 25 17:50:34 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Fri, 25 Feb 2005 20:50:34 -0500 Subject: [seek-kr-sms] ontology/folder UI design in Kepler In-Reply-To: <421FC623.7040509@nceas.ucsb.edu> Message-ID: <000401c51ba5$8f899740$3ca6c684@BTS2K3000D5635086B> Matt>In doing so, we've recognized a bunch of problems with using the informal 'folder' concept to represent an ontology class. SK>I do not think that tree controls are inherently evil, but is it really necessary to use idea of folder??? Prot?g? and GrOWL both have class tree for navigating the ontology, but we have nice icons with letter "C" and it is hard to confuse the classes with folders. Tree is good for navigation but naturally it does not provide a clear ideas about concepts. Matt> The Growl editor is a more acurate representation of the ontology but has limitations given the small space we are trying to use in Kepler to discuss this stuff. SK> GrOWL editor take some space but sometimes it is possible to use a small part of GrOWL. (E.g. GrOWL applet in ESD is far more compact then GrOWL editor) . Adding filters on which I am working now will make GrOWL spiders even more compact and humanly. Hope that within next week I will make filters for class definitions and class instances. So I would suggest to evaluate GrOWL after that. I will create jar and make it easy. In context of Kepler GrOWL could be used as follows: Option#1 Layout: ------------------ Tree Control Window ------------------- Filter Select Combo ------------------- GrOWL Panel, Configured for Close visible locality ---------------------- I presume that this will take 1/3 or 1/2 of the whole Kepler Window on the left or on the right and will be collapsed as soon as selection is done. Option#2 The other possible scenario for using GrOWL may follow the latest fashion that is popular among C++ IDE developers: Have powerful navigator for switching the perspective and keep visible only those panel/window that is currently used. If we follow this philosophy GrOWL could be used as follows: 1. Right click on place/port for which concept selection is required and select respective menu (e.g "Set Semantic Type") This will bring GrOWL window to the top. It does not have to obscure all information about workflow. The information that is relevant to selection may be shown on the top ( eg - the pipeline for which the semantic type is selected and the two actors which are connected by the pipeline) 2. Browse ontology and find the concept. 3. When done - double click on the concept. This should collapse the growl window and bring Kepler to its standard view. In GrOWL I followed this philosophy when made Metadata panel to completely substitute main window when user wants to examine metadata. Option#3 Alternative metaphor for GrOWL usage is file selection dialog. Similar to that we may have "concept selection dialog" which may have layout as: ------------------------------------------ Filter Select Combo| Class Selection Combo ---------------------------------------------- GrOWL Panel, Configured for Close visible locality ----------------------------------------------- Have a nice weekend, serguei From jones at nceas.ucsb.edu Fri Feb 25 17:58:22 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Fri, 25 Feb 2005 16:58:22 -0900 Subject: [seek-kr-sms] running growl from CVS In-Reply-To: <000001c51b9d$d61b5ca0$3ca6c684@BTS2K3000D5635086B> References: <000001c51b9d$d61b5ca0$3ca6c684@BTS2K3000D5635086B> Message-ID: <421FD7BE.1070200@nceas.ucsb.edu> Hey Sergui, I think it is a good idea to have some declaritive build file in place. I would use it, and I'm sure many of the other SEEK developers would too. Plus, they really aren't that hard to configure. You certainly do NOT have to list every .h and .cc file -- rather, you just have to point it at the directory containing the source. You do need to specify the jar file dependencies, but that is worthwhile anyways as it makes it explicit what is needed to build. I added an ant build.xml to CVS that should work if all of the dependencies were satisfied. Update CVS and try running "ant" from the ontobrowser directory. The jar files from Jena 2.1 don't seem to be sufficient. I added them all to the "lib/jar" directory but still get a ton of errors when I compile with ant. So, my guess is that there are dependencies you forgot to mention. If you figure it out, adding those additional jars to "lib/jar" should allow the ant build to work. Eclipse is great (I use it too), but it really is a pain to configure. I just spent 20 minutes trying to get Growl to build, and I still have 779 errors even after including all of the jar files from Jena 2.1 in the build path. Probably the same problem as ant. Thanks, Matt Serguei Krivov wrote: > OK I shall create jar as soon as I get stable version with graphic > filters. I will be refreshing jar with each stable buld. > > Maintaining Ant file on the other hand is about as easy and pleasurable > as manual maintaining of configure file for a large C++ project. One > tends to always forget adding newly created *.h and *.cc files to > configure ( so I always wanted to use IDEs as KDeveloper or Anjuta that > relieve me from maintaining configure files ). Thanks to Eclipse and > Netbeans Ant became completely unnecessary for java developers, users > and testers on the other hand normally do not need to recompile java > code for their specific platform, so neither they need a tool ala > "configure" if jar is provided. > > Having said so, I will create Ant file for GrOWL if there is at least > one developer who would make use of it or if there is at least one > tester who would prefer Ant file to jar. Please let me know... > > serguei > > > > ------------------------------------------------------------------------ > -------------- > Serguei Krivov, Assist. Research Professor, > Computer Science Dept. & Gund Inst. for Ecological Economics, > University of Vermont; 590 Main St. Burlington VT 05405 > phone: (802)-656-2978 > > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Ferdinando > Villa > Sent: Friday, February 25, 2005 5:00 PM > To: 'Shawn Bowers'; 'Serguei Krivov' > Cc: seek-kr-sms at ecoinformatics.org > Subject: RE: [seek-kr-sms] running growl from CVS > > I think an Ant build file could peacefully coexist with the Eclipse > project and wouldn't be so hard to set up, right? And yes, I also think > executable jars (at least for the editor) should be in cvs. > > ferdinando > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Shawn Bowers > Sent: Friday, February 25, 2005 4:59 PM > To: Serguei Krivov > Cc: seek-kr-sms at ecoinformatics.org > Subject: Re: [seek-kr-sms] running growl from CVS > > > > For those of us who like to do it the old-fashioned way; perhaps you > could stick a new GrowlEditor.jar file somewhere (e.g., in cvs) that we > could just run without having to compile, etc. > > thanks, > shawn > > > Serguei Krivov wrote: > >>Hi Matt, >>Sorry for the mess with the code and docs. We intended to clean it >>before the beta release. At this point we are still in the stage of >>alpha. >> >>Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as > > >>a consequence we did not use any separate utility for building >>project. If you do not use eclipse or NB then we have to think how to >>port GrOWL to your type of project. My impression however was that >>most of us who do java use eclipse. >> >>If you have eclipse then compiling with GrOWL/Jena is easy (comparing >>to compiling GrOWL?OWLAPI): 1. Install Jena, or have (ALL)Jena jars >>ready 2.If you are using eclipse CVS check out directory >>kr-sms/ontobrowser/src: >>right click on it, select Check Out As, select Java Project and go >>through the steps that the wizards offer. Assume that the project name >>you selected is "ontobrowser" >>If using external CVS , get the code and create new project e.g. >>"ontobrowser" using directory kr-sms/ontobrowser/src as top directory > > of > >>the project. >> >>3. Project will be compiled with many errors. Get to the "property >>dialog "of the project "ontobrowser" (for this one can right click on >>the project, select "properties" from the bottom of popup menu, or >>select the project in the explorer and then go to Menu: Project | >>Properties) >>In the property dialog click on Java Build Path (on the left). Then >>select pane Libraries, then click button AddExternal Jars and add ALL >>jena jars to the project. After this project should compile. There >>will be still errors in the code related to OWLAPI part, and in the >>old code, but these are negligible. >> >>4. To execute: in package explorer select >>org/ecoinformatics/seek/growl/editor/GrowlEditor.java >>then in menu Run select: Run As | Java Application >> >> >>If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for >>code, Add the same external jars of Jena. >> >>Please let me know if more detailed description could be more useful. >> >>At the moment browsing of large ontologies is not really great. I am >>working on graphic filters that would allow to select a class and >>view separately a)its definition, b)its instances, c) references to >>this class etc . After this is done (by next week) browsing of large >>ontologies will be easy. >> >> >>serguei >> >> >> >> >> >> >> >> >>-----Original Message----- >>From: seek-kr-sms-admin at ecoinformatics.org >>[mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones >>Sent: Friday, February 25, 2005 4:00 PM >>To: Sergui Krivov >>Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org >>Subject: [seek-kr-sms] running growl from CVS >> >>Sergui, >> >>I'm trying to look at the new growl from CVS. We'd like to evaluate >>how >> >>it might be used in Kepler for ontology UI stuff. Unfortunately, >>here's no readme, docs, ant build file (build.xml), makefile, batch >>file, or shell script that's relevant as far as I can tell in the >>ontobrowser directory. Can you help me out? >> >>1) Is the source in "seek/projects/kr-sms/ontobrowser" ? >>2) How do I build Growl from source? >>3) How do I run Growl once built? >> >>Thanks. >> >>Matt >> > > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- From Serguei.Krivov at uvm.edu Sat Feb 26 00:53:47 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Sat, 26 Feb 2005 03:53:47 -0500 Subject: [seek-kr-sms] running growl from CVS In-Reply-To: <421FD7BE.1070200@nceas.ucsb.edu> Message-ID: <000001c51be0$afc16ac0$3ca6c684@BTS2K3000D5635086B> Hey Matt, Thanks for putting in the Ant file. I moved the OWLAPI code to separate folder and added attribute: excludes="edu/**, org/ecoinformatics/seek/gfl/**, org/ecoinformatics/seek/growl/applet/**, org/ecoinformatics/seek/growl/owlapi/**" to the target "compile". Now I can compile things with Ant but I still have 2 problems: 1. run script is not created by Ant(so I added one manually to .../lib/jar) 2. I have images in org/ecoinformatics/seek/growl/images that should go into growl.jar as ressources, but they do not. I wonder if there is any way to put them without copyng them one by one? I could not extract any information on this subject from http://ant.apache.org/manual/index.html . Could you possibly point me to any documentations that explains how to do that? Thanks, serguei -----Original Message----- From: seek-kr-sms-admin at ecoinformatics.org [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones Sent: Friday, February 25, 2005 8:58 PM To: Serguei Krivov Cc: seek-kr-sms at ecoinformatics.org Subject: Re: [seek-kr-sms] running growl from CVS Hey Sergui, I think it is a good idea to have some declaritive build file in place. I would use it, and I'm sure many of the other SEEK developers would too. Plus, they really aren't that hard to configure. You certainly do NOT have to list every .h and .cc file -- rather, you just have to point it at the directory containing the source. You do need to specify the jar file dependencies, but that is worthwhile anyways as it makes it explicit what is needed to build. I added an ant build.xml to CVS that should work if all of the dependencies were satisfied. Update CVS and try running "ant" from the ontobrowser directory. The jar files from Jena 2.1 don't seem to be sufficient. I added them all to the "lib/jar" directory but still get a ton of errors when I compile with ant. So, my guess is that there are dependencies you forgot to mention. If you figure it out, adding those additional jars to "lib/jar" should allow the ant build to work. Eclipse is great (I use it too), but it really is a pain to configure. I just spent 20 minutes trying to get Growl to build, and I still have 779 errors even after including all of the jar files from Jena 2.1 in the build path. Probably the same problem as ant. Thanks, Matt Serguei Krivov wrote: > OK I shall create jar as soon as I get stable version with graphic > filters. I will be refreshing jar with each stable buld. > > Maintaining Ant file on the other hand is about as easy and pleasurable > as manual maintaining of configure file for a large C++ project. One > tends to always forget adding newly created *.h and *.cc files to > configure ( so I always wanted to use IDEs as KDeveloper or Anjuta that > relieve me from maintaining configure files ). Thanks to Eclipse and > Netbeans Ant became completely unnecessary for java developers, users > and testers on the other hand normally do not need to recompile java > code for their specific platform, so neither they need a tool ala > "configure" if jar is provided. > > Having said so, I will create Ant file for GrOWL if there is at least > one developer who would make use of it or if there is at least one > tester who would prefer Ant file to jar. Please let me know... > > serguei > > > > ------------------------------------------------------------------------ > -------------- > Serguei Krivov, Assist. Research Professor, > Computer Science Dept. & Gund Inst. for Ecological Economics, > University of Vermont; 590 Main St. Burlington VT 05405 > phone: (802)-656-2978 > > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Ferdinando > Villa > Sent: Friday, February 25, 2005 5:00 PM > To: 'Shawn Bowers'; 'Serguei Krivov' > Cc: seek-kr-sms at ecoinformatics.org > Subject: RE: [seek-kr-sms] running growl from CVS > > I think an Ant build file could peacefully coexist with the Eclipse > project and wouldn't be so hard to set up, right? And yes, I also think > executable jars (at least for the editor) should be in cvs. > > ferdinando > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Shawn Bowers > Sent: Friday, February 25, 2005 4:59 PM > To: Serguei Krivov > Cc: seek-kr-sms at ecoinformatics.org > Subject: Re: [seek-kr-sms] running growl from CVS > > > > For those of us who like to do it the old-fashioned way; perhaps you > could stick a new GrowlEditor.jar file somewhere (e.g., in cvs) that we > could just run without having to compile, etc. > > thanks, > shawn > > > Serguei Krivov wrote: > >>Hi Matt, >>Sorry for the mess with the code and docs. We intended to clean it >>before the beta release. At this point we are still in the stage of >>alpha. >> >>Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as > > >>a consequence we did not use any separate utility for building >>project. If you do not use eclipse or NB then we have to think how to >>port GrOWL to your type of project. My impression however was that >>most of us who do java use eclipse. >> >>If you have eclipse then compiling with GrOWL/Jena is easy (comparing >>to compiling GrOWL?OWLAPI): 1. Install Jena, or have (ALL)Jena jars >>ready 2.If you are using eclipse CVS check out directory >>kr-sms/ontobrowser/src: >>right click on it, select Check Out As, select Java Project and go >>through the steps that the wizards offer. Assume that the project name >>you selected is "ontobrowser" >>If using external CVS , get the code and create new project e.g. >>"ontobrowser" using directory kr-sms/ontobrowser/src as top directory > > of > >>the project. >> >>3. Project will be compiled with many errors. Get to the "property >>dialog "of the project "ontobrowser" (for this one can right click on >>the project, select "properties" from the bottom of popup menu, or >>select the project in the explorer and then go to Menu: Project | >>Properties) >>In the property dialog click on Java Build Path (on the left). Then >>select pane Libraries, then click button AddExternal Jars and add ALL >>jena jars to the project. After this project should compile. There >>will be still errors in the code related to OWLAPI part, and in the >>old code, but these are negligible. >> >>4. To execute: in package explorer select >>org/ecoinformatics/seek/growl/editor/GrowlEditor.java >>then in menu Run select: Run As | Java Application >> >> >>If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for >>code, Add the same external jars of Jena. >> >>Please let me know if more detailed description could be more useful. >> >>At the moment browsing of large ontologies is not really great. I am >>working on graphic filters that would allow to select a class and >>view separately a)its definition, b)its instances, c) references to >>this class etc . After this is done (by next week) browsing of large >>ontologies will be easy. >> >> >>serguei >> >> >> >> >> >> >> >> >>-----Original Message----- >>From: seek-kr-sms-admin at ecoinformatics.org >>[mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones >>Sent: Friday, February 25, 2005 4:00 PM >>To: Sergui Krivov >>Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org >>Subject: [seek-kr-sms] running growl from CVS >> >>Sergui, >> >>I'm trying to look at the new growl from CVS. We'd like to evaluate >>how >> >>it might be used in Kepler for ontology UI stuff. Unfortunately, >>here's no readme, docs, ant build file (build.xml), makefile, batch >>file, or shell script that's relevant as far as I can tell in the >>ontobrowser directory. Can you help me out? >> >>1) Is the source in "seek/projects/kr-sms/ontobrowser" ? >>2) How do I build Growl from source? >>3) How do I run Growl once built? >> >>Thanks. >> >>Matt >> > > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- _______________________________________________ seek-kr-sms mailing list seek-kr-sms at ecoinformatics.org http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From Serguei.Krivov at uvm.edu Sat Feb 26 03:24:31 2005 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Sat, 26 Feb 2005 06:24:31 -0500 Subject: [seek-kr-sms] growl/ant In-Reply-To: <000001c51be0$afc16ac0$3ca6c684@BTS2K3000D5635086B> Message-ID: <000001c51bf5$bdf75e50$3ca6c684@BTS2K3000D5635086B> Matt, It seems that I resolved the problem just by trial and error. The built.xml that is in CVS compiles and runs growl. So the growl1.bat runs the jar in ontobrowser/lib directory using Jena files in ontobrowser/lib/jar. But my results with Ant were so far non-deterministic as if sometimes it works and then after restarting eclipse does not. Thanks again for helping with ant file. serguei Hey Matt, Thanks for putting in the Ant file. I moved the OWLAPI code to separate folder and added attribute: excludes="edu/**, org/ecoinformatics/seek/gfl/**, org/ecoinformatics/seek/growl/applet/**, org/ecoinformatics/seek/growl/owlapi/**" to the target "compile". Now I can compile things with Ant but I still have 2 problems: 1. run script is not created by Ant(so I added one manually to .../lib/jar) 2. I have images in org/ecoinformatics/seek/growl/images that should go into growl.jar as ressources, but they do not. I wonder if there is any way to put them without copyng them one by one? I could not extract any information on this subject from http://ant.apache.org/manual/index.html . Could you possibly point me to any documentations that explains how to do that? Thanks, serguei -----Original Message----- From: seek-kr-sms-admin at ecoinformatics.org [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones Sent: Friday, February 25, 2005 8:58 PM To: Serguei Krivov Cc: seek-kr-sms at ecoinformatics.org Subject: Re: [seek-kr-sms] running growl from CVS Hey Sergui, I think it is a good idea to have some declaritive build file in place. I would use it, and I'm sure many of the other SEEK developers would too. Plus, they really aren't that hard to configure. You certainly do NOT have to list every .h and .cc file -- rather, you just have to point it at the directory containing the source. You do need to specify the jar file dependencies, but that is worthwhile anyways as it makes it explicit what is needed to build. I added an ant build.xml to CVS that should work if all of the dependencies were satisfied. Update CVS and try running "ant" from the ontobrowser directory. The jar files from Jena 2.1 don't seem to be sufficient. I added them all to the "lib/jar" directory but still get a ton of errors when I compile with ant. So, my guess is that there are dependencies you forgot to mention. If you figure it out, adding those additional jars to "lib/jar" should allow the ant build to work. Eclipse is great (I use it too), but it really is a pain to configure. I just spent 20 minutes trying to get Growl to build, and I still have 779 errors even after including all of the jar files from Jena 2.1 in the build path. Probably the same problem as ant. Thanks, Matt Serguei Krivov wrote: > OK I shall create jar as soon as I get stable version with graphic > filters. I will be refreshing jar with each stable buld. > > Maintaining Ant file on the other hand is about as easy and pleasurable > as manual maintaining of configure file for a large C++ project. One > tends to always forget adding newly created *.h and *.cc files to > configure ( so I always wanted to use IDEs as KDeveloper or Anjuta that > relieve me from maintaining configure files ). Thanks to Eclipse and > Netbeans Ant became completely unnecessary for java developers, users > and testers on the other hand normally do not need to recompile java > code for their specific platform, so neither they need a tool ala > "configure" if jar is provided. > > Having said so, I will create Ant file for GrOWL if there is at least > one developer who would make use of it or if there is at least one > tester who would prefer Ant file to jar. Please let me know... > > serguei > > > > ------------------------------------------------------------------------ > -------------- > Serguei Krivov, Assist. Research Professor, > Computer Science Dept. & Gund Inst. for Ecological Economics, > University of Vermont; 590 Main St. Burlington VT 05405 > phone: (802)-656-2978 > > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Ferdinando > Villa > Sent: Friday, February 25, 2005 5:00 PM > To: 'Shawn Bowers'; 'Serguei Krivov' > Cc: seek-kr-sms at ecoinformatics.org > Subject: RE: [seek-kr-sms] running growl from CVS > > I think an Ant build file could peacefully coexist with the Eclipse > project and wouldn't be so hard to set up, right? And yes, I also think > executable jars (at least for the editor) should be in cvs. > > ferdinando > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Shawn Bowers > Sent: Friday, February 25, 2005 4:59 PM > To: Serguei Krivov > Cc: seek-kr-sms at ecoinformatics.org > Subject: Re: [seek-kr-sms] running growl from CVS > > > > For those of us who like to do it the old-fashioned way; perhaps you > could stick a new GrowlEditor.jar file somewhere (e.g., in cvs) that we > could just run without having to compile, etc. > > thanks, > shawn > > > Serguei Krivov wrote: > >>Hi Matt, >>Sorry for the mess with the code and docs. We intended to clean it >>before the beta release. At this point we are still in the stage of >>alpha. >> >>Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as > > >>a consequence we did not use any separate utility for building >>project. If you do not use eclipse or NB then we have to think how to >>port GrOWL to your type of project. My impression however was that >>most of us who do java use eclipse. >> >>If you have eclipse then compiling with GrOWL/Jena is easy (comparing >>to compiling GrOWL?OWLAPI): 1. Install Jena, or have (ALL)Jena jars >>ready 2.If you are using eclipse CVS check out directory >>kr-sms/ontobrowser/src: >>right click on it, select Check Out As, select Java Project and go >>through the steps that the wizards offer. Assume that the project name >>you selected is "ontobrowser" >>If using external CVS , get the code and create new project e.g. >>"ontobrowser" using directory kr-sms/ontobrowser/src as top directory > > of > >>the project. >> >>3. Project will be compiled with many errors. Get to the "property >>dialog "of the project "ontobrowser" (for this one can right click on >>the project, select "properties" from the bottom of popup menu, or >>select the project in the explorer and then go to Menu: Project | >>Properties) >>In the property dialog click on Java Build Path (on the left). Then >>select pane Libraries, then click button AddExternal Jars and add ALL >>jena jars to the project. After this project should compile. There >>will be still errors in the code related to OWLAPI part, and in the >>old code, but these are negligible. >> >>4. To execute: in package explorer select >>org/ecoinformatics/seek/growl/editor/GrowlEditor.java >>then in menu Run select: Run As | Java Application >> >> >>If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for >>code, Add the same external jars of Jena. >> >>Please let me know if more detailed description could be more useful. >> >>At the moment browsing of large ontologies is not really great. I am >>working on graphic filters that would allow to select a class and >>view separately a)its definition, b)its instances, c) references to >>this class etc . After this is done (by next week) browsing of large >>ontologies will be easy. >> >> >>serguei >> >> >> >> >> >> >> >> >>-----Original Message----- >>From: seek-kr-sms-admin at ecoinformatics.org >>[mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones >>Sent: Friday, February 25, 2005 4:00 PM >>To: Sergui Krivov >>Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org >>Subject: [seek-kr-sms] running growl from CVS >> >>Sergui, >> >>I'm trying to look at the new growl from CVS. We'd like to evaluate >>how >> >>it might be used in Kepler for ontology UI stuff. Unfortunately, >>here's no readme, docs, ant build file (build.xml), makefile, batch >>file, or shell script that's relevant as far as I can tell in the >>ontobrowser directory. Can you help me out? >> >>1) Is the source in "seek/projects/kr-sms/ontobrowser" ? >>2) How do I build Growl from source? >>3) How do I run Growl once built? >> >>Thanks. >> >>Matt >> > > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- _______________________________________________ seek-kr-sms mailing list seek-kr-sms at ecoinformatics.org http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms _______________________________________________ seek-kr-sms mailing list seek-kr-sms at ecoinformatics.org http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From ferdinando.villa at uvm.edu Sat Feb 26 19:15:29 2005 From: ferdinando.villa at uvm.edu (Ferdinando Villa) Date: Sat, 26 Feb 2005 22:15:29 -0500 Subject: [seek-kr-sms] ontology/folder UI design in Kepler In-Reply-To: <421FC623.7040509@nceas.ucsb.edu> References: <421FC623.7040509@nceas.ucsb.edu> Message-ID: <1109474129.4591.15.camel@basil.snr.uvm.edu> Hi folks, reading through the chat I was wondering that maybe something like Serguei's idea of 'graphic extension' may be helpful here. Graphic extension (I'm sure there's a better name) associate a fragment of knowledge from an ontology with a particular display mode, graphic symbol or whatever - e.g. different-looking arrows, folder icons, or stock/flow symbols a' la Stella. Used within an interface that's capable of handling them, they can be used to interface a conceptual model tailored to a specific user to the actual ontology it uses, hiding its complexities. Serguei has put some examples online, see e.g. http://ecoinformatics.uvm.edu/dmaps/tut42.html http://ecoinformatics.uvm.edu/dmaps/tut43.html It's something we're planning to integrate into GrOWL, to build generalized modeling environments where after you load the mapping (as an OWL file) you can use domain-specific icons and create instances whose actual OWL definition is more complex than it looks. Users see an intuitive/familiar graphical depiction of their domains, but the machine thinks OWL internally. E.g. this can be used to build Stella on top of GrOWL, and have it output full OWL specifications of the models. I'm leaving for a few days and writing this in a hurry - anyway, any chance that this concept (as is or used with GrOWL) can help integrating KR into Kepler? It could be used, for example, to help users define new concepts that extend others in ways more complex than simple subsumption, without having to properly link them to an ontology that they have no chance of understanding well enough to do it right. ciao, ferdinando On Fri, 2005-02-25 at 19:43, Matt Jones wrote: > Messed up the list address ... sending again... sorry for the duplicate > laura. > > Matt > > -------- Original message ------------------ > Hi Laura, > > Chad, Shawn, and I have been discussing the tree control on the left > side of the Kepler window. Chad and Shawn are currently modifying it to > allow creation of new nodes in the ontology. In doing so, we've > recognized a bunch of problems with using the informal 'folder' concept > to represent an ontology class. The Growl editor is a more acurate > representation of the ontology but has limitations given the small space > we are trying to use in Kepler to discuss this stuff. We need to > resolve this to make the UI clear and not have the users mess up the > ontology as they add new concepts and actors. The attached log of our > IRC conversation describes some of the issues. Could you review it, and > then we can discuss how to reach our goal. I think its important to > have you involved at this design stage. Chad and Shawn are implementing > now so we need to provide feedback asap. Maybe we can have a conference > call next week? Thanks. > > Matt -- Ferdinando Villa, Ph.D., Associate Research Professor, Ecoinformatics Gund Institute for Ecological Economics and Dept of Botany, Univ. of Vermont http://ecoinformatics.uvm.edu From ludaesch at ucdavis.edu Sun Feb 27 10:57:59 2005 From: ludaesch at ucdavis.edu (Bertram Ludaescher) Date: Sun, 27 Feb 2005 10:57:59 -0800 Subject: [seek-kr-sms] a presentation on data integration In-Reply-To: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> References: <000001c5144a$b1fab460$3ca6c684@BTS2K3000D5635086B> Message-ID: <16930.6199.121000.531087@gargle.gargle.HOWL> Serguei: I finally got a chance to take a brief look at this. Very nice presentation and summary of the work on data integration/query rewriting using constraints. See also the tutorial given and PODS (which doesn't focus on the P2P case and thus makes a nice "supplement" to the presentation you sent): http://www.dis.uniroma1.it/~lenzerin/homepagine/talks/TutorialPODS02.pdf These should be made mandatory reading for folks implementing data integration systems! ;-) Bertram Serguei Krivov writes: > Here is a 2005 presentation on data integration from Slovak Republic- > http://www.sofsem.sk/presentations/sofsem05-lenzerini.pdf > Seems it is very close to Shawns & Bertrams work, save it is based more > on FOL > > serguei > From ludaesch at ucdavis.edu Sun Feb 27 11:05:24 2005 From: ludaesch at ucdavis.edu (Bertram Ludaescher) Date: Sun, 27 Feb 2005 11:05:24 -0800 Subject: [seek-kr-sms] [Fwd: [Fwd: Ecoterm environmental terminology mtg]] In-Reply-To: <1109110869.5622.9.camel@phmlaptop> References: <421B807A.7010809@nceas.ucsb.edu> <1109110869.5622.9.camel@phmlaptop> Message-ID: <16930.6644.982000.437664@gargle.gargle.HOWL> I wouldn't have minded going to Germany ;-) but can't travel during this time, unfortunately.. Bertram Peter McCartney writes: > their website seems to inidicat a lot of activities that overlap with > our community, although its hard to tell how mature many of them are. > the immediate workshop topic is directly relevant and timely though. i > think someone should go. > > On Tue, 2005-02-22 at 09:56 -0900, Matt Jones wrote: > > Forwarding again, got the seek-kr-sms address wrong last time. Oops. > > > > Matt > > > > email message attachment ([Fwd: Ecoterm environmental terminology > > mtg]) > > On Tue, 2005-02-22 at 09:56 -0900, Matt Jones wrote: > > > Hi Mark, > > > > > > This meeting seemed relevant to the KR and maybe SMS groups. Gail > > > Hodges used to be involved in the Ceres/NBII thesaurus project, and now > > > appears to be in the EU. I also hadn't seen this Ecoinformatics > > > Initiative web site before. Interesting. Do you think we should send > > > anyone over that has knowledge of our ontologies? > > > > > > Matt > > > > > > > > > email message attachment (INVITATION: 2nd ECOTERM MEETING ON > > > ADVANCING ENVIRONMENTAL TERMINOLOGY) > > > On Tue, 2005-02-22 at 09:56 -0900, Matt Jones wrote: > > > > SOME OF YOU RECEIVED AN INVITATION TO A MORE LIMITED VERSION OF > > > > THIS MEETING LAST YEAR IN GENEVA BUT WEREN'T ABLE TO ATTEND. WE > > > > HOPE THAT YOU WILL BE ABLE TO JOIN US THIS YEAR. NEW GROUP MEMBERS > > > > ARE ALWAYS WELCOME. > > > > > > > > PLEASE FEEL FREE TO DISTRIBUTE TO OTHERS WHO MIGHT BE INTERESTED. > > > > THIS IS BEING DISTRIBUTED TO SEVERAL LISTS. APOLOGIES IN ADVANCE > > > > FOR DUPLICATION. > > > > > > > > ANNOUNCING THE 2ND ECOTERM MEETING > > > > The German Federal Environment Agency > > > > (UBA- Umweltbundesamt) > > > > Offices 1, Berlin Grunewald > > > > Bismarckplatz 1, > > > > Berlin, Germany > > > > 15 April 2005 > > > > > > > > > > > > In April 2004 the Ecoterm Group was formed by parties interested > > > > in working together on environmental terminologies, their > > > > integration and their use with semantic web technologies. The > > > > Ecoterm Group is a working group of the Ecoinformatics Initiative > > > > (http://ecoinfo.eionet.eu.int/ ). > > > > > > > > The second meeting of the Ecoterm Group will take place at the UBA > > > > in Berlin on 15 April 2005. > > > > > > > > The agenda will include an update on the activities that resulted > > > > from the Ecoterm Meeting in Geneva in April 2004, updates on > > > > individual projects from the participants, and an update on > > > > progress in relevant standards and tool development. A formal > > > > agenda is still being prepared. > > > > > > > > There is no registration cost. Meals will be on your own. > > > > > > > > Please register at http://ecoterm.infointl.com > > > > Note that this registration form will not register you for the > > > > OpenForum. (See the OpenForum information below.) > > > > > > > > You can find information about the location of UBA at: > > > > http://www.umweltdaten.de/down-e/anreise.pdf > > > > > > > > > > > > >From Crowne Plaza, the location for the OpenForum, you can reach > > > > UBA within 20 minutes with Bus X10. The following hotels are very > > > > close to UBA (within 10 minutes of walking distance) should you > > > > choose to be closer to the location for the Ecoterm Meeting: > > > > http://www.kronprinz-hotel.de/ > > > > > > > > and > > > > http://www.hotel-haus-bismarck.de/index.html > > > > > > > > > > > > The meeting will take place the day after the Open Forum on > > > > Metadata Registries, which will include a significant number of > > > > terminology related presentations. We encourage you to come early > > > > and attend the Open Forum. The topic, "Semantic Interoperability: > > > > Where Meaning Meets Metadata" will be very relevant to our > > > > discussions on Friday. Information about the Open Forum, > > > > including hotel reservations, can be found at > > > > http://www.berlinopenforum.de/. Note that the OpenForum > > > > registration form will not register you for the Ecoterm Meeting. > > > > (See the registration information above.) We encourage you to come > > > > early and attend the OpenForum. > > > > > > > > We look forward to seeing you in Berlin. > > > > > > > > Gail Hodge > > > > Ecoterm Meeting Organizer > > > > > > > > Sr. Information Scientist > > > > Consultant to the US Geological Survey > > > > Information International Associates, Inc. > > > > 312 Walnut Place > > > > Havertown, Pennsylvania 19083 USA > > > > +1 865-742-5430 (cell) > > > > +1 865-481-0390 (fax) > > > > gailhodge at aol.com > > > > > > > > > > > > > > > > > _______________________________________________ > seek-kr-sms mailing list > seek-kr-sms at ecoinformatics.org > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms From jones at nceas.ucsb.edu Mon Feb 28 10:33:13 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Mon, 28 Feb 2005 09:33:13 -0900 Subject: [seek-kr-sms] Re: growl/ant In-Reply-To: <000001c51bf5$bdf75e50$3ca6c684@BTS2K3000D5635086B> References: <000001c51bf5$bdf75e50$3ca6c684@BTS2K3000D5635086B> Message-ID: <422363E9.7000807@nceas.ucsb.edu> Thanks Sergui, I was able to run it. From ant, you can just do "ant growl" to run it, which compiles, installs, and runs it. I also added a unix shell script to run it from linux. I moved the batch file and the shell script to the top level ontobrowser directory so that they can be more easily found. I also added a brief README.txt -- could you look it over and edit as needed. Thanks. Matt Serguei Krivov wrote: > Matt, > It seems that I resolved the problem just by trial and error. The > built.xml that is in CVS compiles and runs growl. So the growl1.bat > runs the jar in ontobrowser/lib directory using Jena files in > ontobrowser/lib/jar. But my results with Ant were so far > non-deterministic as if sometimes it works and then after restarting > eclipse does not. > > Thanks again for helping with ant file. > serguei > > Hey Matt, > > Thanks for putting in the Ant file. I moved the OWLAPI code to separate > folder and added attribute: > excludes="edu/**, org/ecoinformatics/seek/gfl/**, > org/ecoinformatics/seek/growl/applet/**, > org/ecoinformatics/seek/growl/owlapi/**" > to the target "compile". Now I can compile things with Ant but I still > have 2 problems: > > 1. run script is not created by Ant(so I added one manually to > .../lib/jar) > 2. I have images in org/ecoinformatics/seek/growl/images that should go > into growl.jar as ressources, but they do not. I wonder if there is any > way to put them without copyng them one by one? > > I could not extract any information on this subject from > http://ant.apache.org/manual/index.html . Could you possibly point me to > any documentations that explains how to do that? > > Thanks, > serguei > > > -----Original Message----- > From: seek-kr-sms-admin at ecoinformatics.org > [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones > Sent: Friday, February 25, 2005 8:58 PM > To: Serguei Krivov > Cc: seek-kr-sms at ecoinformatics.org > Subject: Re: [seek-kr-sms] running growl from CVS > > Hey Sergui, > > I think it is a good idea to have some declaritive build file in place. > I would use it, and I'm sure many of the other SEEK developers would > too. Plus, they really aren't that hard to configure. You certainly do > > NOT have to list every .h and .cc file -- rather, you just have to point > > it at the directory containing the source. You do need to specify the > jar file dependencies, but that is worthwhile anyways as it makes it > explicit what is needed to build. > > I added an ant build.xml to CVS that should work if all of the > dependencies were satisfied. Update CVS and try running "ant" from the > ontobrowser directory. The jar files from Jena 2.1 don't seem to be > sufficient. I added them all to the "lib/jar" directory but still get a > > ton of errors when I compile with ant. So, my guess is that there are > dependencies you forgot to mention. If you figure it out, adding those > additional jars to "lib/jar" should allow the ant build to work. > > Eclipse is great (I use it too), but it really is a pain to configure. > I just spent 20 minutes trying to get Growl to build, and I still have > 779 errors even after including all of the jar files from Jena 2.1 in > the build path. Probably the same problem as ant. > > Thanks, > > Matt > > Serguei Krivov wrote: > >>OK I shall create jar as soon as I get stable version with graphic >>filters. I will be refreshing jar with each stable buld. >> >>Maintaining Ant file on the other hand is about as easy and > > pleasurable > >>as manual maintaining of configure file for a large C++ project. One >>tends to always forget adding newly created *.h and *.cc files to >>configure ( so I always wanted to use IDEs as KDeveloper or Anjuta > > that > >>relieve me from maintaining configure files ). Thanks to Eclipse and >>Netbeans Ant became completely unnecessary for java developers, users >>and testers on the other hand normally do not need to recompile java >>code for their specific platform, so neither they need a tool ala >>"configure" if jar is provided. >> >>Having said so, I will create Ant file for GrOWL if there is at least >>one developer who would make use of it or if there is at least one >>tester who would prefer Ant file to jar. Please let me know... >> >>serguei >> >> >> >> > > ------------------------------------------------------------------------ > >>-------------- >>Serguei Krivov, Assist. Research Professor, >>Computer Science Dept. & Gund Inst. for Ecological Economics, >>University of Vermont; 590 Main St. Burlington VT 05405 >>phone: (802)-656-2978 >> >> >>-----Original Message----- >>From: seek-kr-sms-admin at ecoinformatics.org >>[mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Ferdinando >>Villa >>Sent: Friday, February 25, 2005 5:00 PM >>To: 'Shawn Bowers'; 'Serguei Krivov' >>Cc: seek-kr-sms at ecoinformatics.org >>Subject: RE: [seek-kr-sms] running growl from CVS >> >>I think an Ant build file could peacefully coexist with the Eclipse >>project and wouldn't be so hard to set up, right? And yes, I also > > think > >>executable jars (at least for the editor) should be in cvs. >> >>ferdinando >> >>-----Original Message----- >>From: seek-kr-sms-admin at ecoinformatics.org >>[mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Shawn > > Bowers > >>Sent: Friday, February 25, 2005 4:59 PM >>To: Serguei Krivov >>Cc: seek-kr-sms at ecoinformatics.org >>Subject: Re: [seek-kr-sms] running growl from CVS >> >> >> >>For those of us who like to do it the old-fashioned way; perhaps you >>could stick a new GrowlEditor.jar file somewhere (e.g., in cvs) that > > we > >>could just run without having to compile, etc. >> >>thanks, >>shawn >> >> >>Serguei Krivov wrote: >> >> >>>Hi Matt, >>>Sorry for the mess with the code and docs. We intended to clean it >>>before the beta release. At this point we are still in the stage of >>>alpha. >>> >>>Both Rich and I are fans of nice IDEs, e.g. Eclipse or NetBeans and as >> >> >>>a consequence we did not use any separate utility for building >>>project. If you do not use eclipse or NB then we have to think how to >>>port GrOWL to your type of project. My impression however was that >>>most of us who do java use eclipse. >>> >>>If you have eclipse then compiling with GrOWL/Jena is easy (comparing >>>to compiling GrOWL?OWLAPI): 1. Install Jena, or have (ALL)Jena jars >>>ready 2.If you are using eclipse CVS check out directory >>>kr-sms/ontobrowser/src: >>>right click on it, select Check Out As, select Java Project and go >>>through the steps that the wizards offer. Assume that the project name >>>you selected is "ontobrowser" >>>If using external CVS , get the code and create new project e.g. >>>"ontobrowser" using directory kr-sms/ontobrowser/src as top directory >> >>of >> >> >>>the project. >>> >>>3. Project will be compiled with many errors. Get to the "property >>>dialog "of the project "ontobrowser" (for this one can right click on >>>the project, select "properties" from the bottom of popup menu, or >>>select the project in the explorer and then go to Menu: Project | >>>Properties) >>>In the property dialog click on Java Build Path (on the left). Then >>>select pane Libraries, then click button AddExternal Jars and add ALL >>>jena jars to the project. After this project should compile. There >>>will be still errors in the code related to OWLAPI part, and in the >>>old code, but these are negligible. >>> >>>4. To execute: in package explorer select >>>org/ecoinformatics/seek/growl/editor/GrowlEditor.java >>>then in menu Run select: Run As | Java Application >>> >>> >>>If you use NetBeans , use kr-sms/ontobrowser/src as a mount point for >>>code, Add the same external jars of Jena. >>> >>>Please let me know if more detailed description could be more useful. >>> >>>At the moment browsing of large ontologies is not really great. I am >>>working on graphic filters that would allow to select a class and >>>view separately a)its definition, b)its instances, c) references to >>>this class etc . After this is done (by next week) browsing of large >>>ontologies will be easy. >>> >>> >>>serguei >>> >>> >>> >>> >>> >>> >>> >>> >>>-----Original Message----- >>>From: seek-kr-sms-admin at ecoinformatics.org >>>[mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones >>>Sent: Friday, February 25, 2005 4:00 PM >>>To: Sergui Krivov >>>Cc: Ferdinando Villa; seek-kr-sms at ecoinformatics.org >>>Subject: [seek-kr-sms] running growl from CVS >>> >>>Sergui, >>> >>>I'm trying to look at the new growl from CVS. We'd like to evaluate >>>how >>> >>>it might be used in Kepler for ontology UI stuff. Unfortunately, >>>here's no readme, docs, ant build file (build.xml), makefile, batch >>>file, or shell script that's relevant as far as I can tell in the >>>ontobrowser directory. Can you help me out? >>> >>>1) Is the source in "seek/projects/kr-sms/ontobrowser" ? >>>2) How do I build Growl from source? >>>3) How do I run Growl once built? >>> >>>Thanks. >>> >>>Matt >>> >> >> >>_______________________________________________ >>seek-kr-sms mailing list >>seek-kr-sms at ecoinformatics.org >>http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms >> >>_______________________________________________ >>seek-kr-sms mailing list >>seek-kr-sms at ecoinformatics.org >>http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms >> >>_______________________________________________ >>seek-kr-sms mailing list >>seek-kr-sms at ecoinformatics.org >>http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms > > -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- From jones at nceas.ucsb.edu Mon Feb 28 10:45:32 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Mon, 28 Feb 2005 09:45:32 -0900 Subject: [seek-kr-sms] [Fwd: [Dbworld] CFP VLDB Workshop on Ontologies-based techniques for Databases and Information Systems] Message-ID: <422366CC.4080200@nceas.ucsb.edu> Mark, This VLDB workshop is probably a good place to present our SEEK ontology work if you think it would be approapriate by September. Maybe Rich and Shawn would be interested, and maybe it would be a good meeting for a new postdoc assuming we manage to recruit by then. Matt -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- -------------- next part -------------- An embedded message was scrubbed... From: "Martine Collard" Subject: [Dbworld] CFP VLDB Workshop on Ontologies-based techniques for Databases and Information Systems Date: Sun, 27 Feb 2005 11:00:01 -0600 (CST) Size: 9910 Url: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20050228/e499ba57/DbworldCFPVLDBWorkshoponOntologies-basedtechniquesforDatabasesandInformationSystems.eml From jones at nceas.ucsb.edu Mon Feb 28 12:15:19 2005 From: jones at nceas.ucsb.edu (Matt Jones) Date: Mon, 28 Feb 2005 11:15:19 -0900 Subject: [Fwd: Re: [seek-kr-sms] ontology/folder UI design in Kepler] Message-ID: <42237BD7.4090000@nceas.ucsb.edu> forwarding Laura's repsonse to the list.... Matt -------------- next part -------------- An embedded message was scrubbed... From: "Laura L. Downey" Subject: RE: [seek-kr-sms] ontology/folder UI design in Kepler Date: Mon, 28 Feb 2005 13:08:06 -0700 Size: 8484 Url: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20050228/272def31/folderUIdesigninKepler.eml From ldowney at lternet.edu Mon Feb 28 13:19:44 2005 From: ldowney at lternet.edu (Laura L. Downey) Date: Mon, 28 Feb 2005 14:19:44 -0700 Subject: [Fwd: Re: [seek-kr-sms] ontology/folder UI design in Kepler] In-Reply-To: <42237BD7.4090000@nceas.ucsb.edu> Message-ID: Additions to my last response that Matt just forwarded: The more I think about this, the more I'm thinking that an ontology expert/knowledge engineer is the person who should be responsible for maintaining consistency within the ontology instead of us trying to design a UI that takes a very complex task and tries to make it simple for regular Kepler users that are not ontology experts. We still need to offer a way for regular users to simply classify things, but the action of actually putting something correctly into the ontology really needs to be done by a knowledge engineer or ontology expert. To that end I could see offering users that are not ontology experts just the simple keyword/concept list to choose from. This would be akin to letting regular users "register" their new actors or concepts for data, but things wouldn't go officially into the ontology until a knowledge engineer had specifically placed them correctly. We can: 1) consider some advanced feature within Kepler that a knowledge engineer would use to do this, or 2) have the KE export the ontology, work with it in their tool of choice, then import the "updated" ontology back into Kepler. For the interim case, where the new actor is registered but not blessed by the KE yet, we could indicate this in a couple of ways, some variation on the visual appearance of a newly registered actor, or we could have a "registered" folder that holds the new actors until they are correctly placed within the ontology by the knowledge engineer. Laura L. Downey Senior Usability Engineer LTER Network Office Department of Biology, MSC03 2020 1 University of New Mexico Albuquerque, NM 87131-0001 505.277.3157 phone 505.277-2541 fax ldowney at lternet.edu -----Original Message----- From: seek-kr-sms-admin at ecoinformatics.org [mailto:seek-kr-sms-admin at ecoinformatics.org] On Behalf Of Matt Jones Sent: Monday, February 28, 2005 1:15 PM To: seek-kr-sms at ecoinformatics.org Cc: Laura Downey Subject: [Fwd: Re: [seek-kr-sms] ontology/folder UI design in Kepler] forwarding Laura's repsonse to the list.... Matt From sbowers at ucdavis.edu Mon Feb 28 15:42:56 2005 From: sbowers at ucdavis.edu (Shawn Bowers) Date: Mon, 28 Feb 2005 15:42:56 -0800 Subject: [Fwd: Re: [seek-kr-sms] ontology/folder UI design in Kepler] In-Reply-To: <42237BD7.4090000@nceas.ucsb.edu> References: <42237BD7.4090000@nceas.ucsb.edu> Message-ID: <4223AC80.6030401@ucdavis.edu> I just wanted to address your comment: > That said, my first comment is does anyone expect Kepler users to be > knowledgeable about formal ontologies and formal representations of > ontologies? Frankly, from the user profiling I've done and the data I've > gathered so far, I don't. We are already introducing new concepts to them > -- the ecogrid, the whole issue of how metadata is employed and used, and > the workflow mechanism itself. And while at a very abstract level the > notion of scientific workflows is not difficult, the devil is always in the > details and there are many details for users to learn to fully exploit > Kepler. I think that this is (or at least was) exactly one of the "missions" in SEEK: to get scientists involved in creating and using *formal* ontologies. Remember that ontologies are a means to enable one to (more) precisely capture meaning ... which is why they are often difficult to create (one has to really understand their own assumptions, etc.). The other side of the puzzle is that the languages and interfaces that exist for creating ontologies are generally more focused on "engineers", be that so-called "knowledge engineers" or programmers/developers. The same can also be said of Ptolemy and Kepler in its current state (i.e., it is a tool not necessarily for scientists, but for programmers/developers). Ultimately, however, I think we are short-selling the ability of ecologists when we say ontologies are too complex for them: ecologists (like other scientists) currently understand in a very deep way the things they are expert in; and compared with this knowledge, the ontologies a scientist would develop are at best an approximation of this complex knowledge. From my own experience with the EOT meetings, I have found people to be generally excited by not only discussing their own research and knowledge, but also in attempting to formalize this information and being able to communicate it to others. So to answer your question: yes, if we are talking about scientists as users, then we do expect that they are knowledgeable about formal ontologies (this is exactly their knowledge); and no, we do not expect them to be knowledgeable about formal representations of ontologies -- this is precisely the challenge of SEEK and other projects like SEEK wrt ontologies. In general, I sense that as a group we might be somewhat unsure of and do not have a clear vision as to how we want to proceed with ontologies. One approach is as above -- engage scientists and develop tools for scientists to actively participate with and develop their own conceptual models. Another approach is to essentially move away from "formal" (or "structured") conceptual models and instead embrace simpler thesauri or keyword-based approaches ("informal" and "unstructured" ontologies) more akin to digital libraries where little effort is required to create a "knowledge" corpus -- and users do not have to be (nor have the option of being) actively engaged at the "conceptual level" except through essentially undefined keywords.