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[protege-discussion] protege-discussion Digest, Vol 75, Issue 11

Ganesh kumar ganeshkumar1987 at gmail.com
Tue Oct 9 18:13:48 PDT 2012


Hi,
Thanks for your very quick response.
The information you provided is very helpful.

is there a way to do it without copying the .pprj file but to solely depend
on the database alone ?

Thanks so much for you help.

On Wed, Oct 10, 2012 at 2:05 PM, <
protege-discussion-request at lists.stanford.edu> wrote:

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> Today's Topics:
>
>    1. Re: protege-discussion Digest, Vol 75, Issue 10 (Ganesh kumar)
>    2. Re: protege-discussion Digest, Vol 75, Issue 10 (Timothy Redmond)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Oct 2012 13:03:37 +1300
> From: Ganesh kumar <ganeshkumar1987 at gmail.com>
> To: protege-discussion at lists.stanford.edu
> Subject: Re: [protege-discussion] protege-discussion Digest, Vol 75,
>         Issue 10
> Message-ID:
>         <CAKj7cG1KWXcr59Nd4VQdPE8BcTSsXdhbBBd=
> 9BZFFTeU6Oe-bA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Timothy,
>
> Thanks for your response.
> I have decided to use mysql as my backend.
>
> I have a new question like - After I create a new database project, I need
> to open the same project from another location.
> But in Open project menu, I do not see an option to open a project from
> database.
>
> Can you please help me to resolve this issue
>
> Thanks in advance.
>
> On Tue, Oct 9, 2012 at 6:14 AM, <
> protege-discussion-request at lists.stanford.edu> wrote:
>
> > Send protege-discussion mailing list submissions to
> >         protege-discussion at lists.stanford.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >         https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> > or, via email, send a message with subject or body 'help' to
> >         protege-discussion-request at lists.stanford.edu
> >
> > You can reach the person managing the list at
> >         protege-discussion-owner at lists.stanford.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of protege-discussion digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: integration of owl files reg (kala devi ramar)
> >    2. Re: integration of owl files reg (Timothy Redmond)
> >    3. Re: Protege 3.4.8 with oracle database backend (Timothy Redmond)
> >    4. NCBO Webinar: Editing and Publishing OWL 2 and OBO ontologies
> >       with WebProtege and BioPortal (Trish Whetzel)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sun, 7 Oct 2012 20:46:08 -0700 (PDT)
> > From: kala devi ramar <kala_ramar at yahoo.com>
> > To: protege-discussion at lists.stanford.edu
> > Subject: Re: [protege-discussion] integration of owl files reg
> > Message-ID:
> >         <1349667968.11531.YahooMailClassic at web162506.mail.bf1.yahoo.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> >
> >
> >
> > Hello all,
> > I have three owl files in protege.Weather.owl, plants.owl and
> > fertilizer.owl. I want to integrate these files to get some inference.
> for
> > example if temp >30c and humidity>60% and plant name="maize" then use
> > xxxxxxxx fertilizer.
> > Please help me how to do it.
> > ?
> > thank u
> > ?
> > R.kaladevi
> > -------------- next part --------------
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> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 08 Oct 2012 06:58:20 -0700
> > From: Timothy Redmond <tredmond at stanford.edu>
> > To: protege-discussion at lists.stanford.edu
> > Subject: Re: [protege-discussion] integration of owl files reg
> > Message-ID: <5072DBFC.8010802 at stanford.edu>
> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> >
> >
> > Create a new ontology that imports all three ontologies and run the
> > reasoner on that.  Both Protege 3 and Protege 4 have buttons for
> > importing ontologies in their first tab (the Metadata tab and the Active
> > Ontology tab respectively).  If you are interested in using inference, I
> > would recommend Protege 4.
> >
> > -Timothy
> >
> >
> > On 10/07/2012 08:46 PM, kala devi ramar wrote:
> > >
> > >
> > >     Hello all,
> > >     I have three owl files in protege.Weather.owl, plants.owl and
> > >     fertilizer.owl. I want to integrate these files to get some
> > >     inference. for example if temp >30c and humidity>60% and plant
> > >     name="maize" then use xxxxxxxx fertilizer.
> > >     Please help me how to do it.
> > >     thank u
> > >     R.kaladevi
> > >
> > >
> > >
> > > _______________________________________________
> > > protege-discussion mailing list
> > > protege-discussion at lists.stanford.edu
> > > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> > >
> > > Instructions for unsubscribing:
> > http://protege.stanford.edu/doc/faq.html#01a.03
> >
> > -------------- next part --------------
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> > >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 08 Oct 2012 07:19:07 -0700
> > From: Timothy Redmond <tredmond at stanford.edu>
> > To: protege-discussion at lists.stanford.edu
> > Subject: Re: [protege-discussion] Protege 3.4.8 with oracle database
> >         backend
> > Message-ID: <5072E0DB.30108 at stanford.edu>
> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> >
> >
> > The Protege team has not supported the Oracle database for many years
> > now.   There was a post some time ago (years?) where somebody supplied a
> > patch which allowed Protege to work with Oracle.  But I did some google
> > searches and didn't find the post in question.
> >
> > My recommendation would be to use either mysql or postgresql which are
> > both tested nightly.
> >
> > -Timothy
> >
> >
> > On 10/04/2012 02:32 PM, Ganesh kumar wrote:
> > > Hi All,
> > >
> > > Does Anyone have or can share me the path where I can download this
> > > version (3.4.8) of protege source code which works with oracle backend.
> > >
> > >
> > > --
> > > *Warm Regards
> > > Ganesh Kumar S
> > > 0064212388360
> > > *
> > >
> > >
> > > _______________________________________________
> > > protege-discussion mailing list
> > > protege-discussion at lists.stanford.edu
> > > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> > >
> > > Instructions for unsubscribing:
> > http://protege.stanford.edu/doc/faq.html#01a.03
> >
> > -------------- next part --------------
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> > >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Mon, 8 Oct 2012 10:14:32 -0700
> > From: Trish Whetzel <plwhetzel at gmail.com>
> > To: protege-discussion at lists.stanford.edu
> > Subject: [protege-discussion] NCBO Webinar: Editing and Publishing OWL
> >         2 and OBO ontologies with WebProtege and BioPortal
> > Message-ID:
> >         <CAE4f=nh=ecD7Xz66aQa4tW5M1hnSGYKs-aad8=5=_
> > 1QkD3yKMA at mail.gmail.com>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > The next NCBO Webinar will be presented by Tania Tudorache and Matthew
> > Horridge from Stanford University on "Editing and Publishing OWL 2 and
> OBO
> > ontologies with WebProt?g? and BioPortal" at 10:00am PDT, Wednesday, Oct.
> > 10.  Below is information on how to join the online meeting via WebEx and
> > accompanying teleconference. For the full schedule of the NCBO Webinar
> > presentations see: http://www.bioontology.org/webinar-series.
> >
> >
> > ABSTRACT:
> > WebProt?g? is a collaborative ontology and knowledge base editor for the
> > Web.  In this talk, we will present the latest WebProt?g? developments,
> > including support for the editing of OWL 2 and OBO ontologies, the new
> > OWL-API backend and the the various collaboration features. We will
> > describe how WebProt?g? can be customized as a domain-expert friendly
> tool
> > and show the OBO specific user interface widgets that are optimized for
> > editing components of OBO ontologies.  We will demonstrate how users can
> > upload and download ontologies, share them with collaborators, and
> > simultaneously edit and comment on them. All ontology changes are
> recorded,
> > and can be inspected by editors, curators or reviewers.  We will also
> show
> > how users can collaborate using the notes and discussions features, as
> well
> > as the watches and notifications functionality.  Finally, we will
> > demonstrate how WebProt?g? integrates with BioPortal services so that,
> for
> > example, users can search for and reference terms in BioPortal ontologies
> > at the click of a mouse.  We will conclude with our plans for the future
> > development of WebProt?g? and its integration with BioPortal.
> >
> >
> > SPEAKER BIOS:
> > Tania Tudorache is a research scientist in the Stanford Center for
> > Biomedical Informatics Research. Her main research interest is the
> > collaborative development of ontologies applied to the biomedical domain.
> > Dr. Tudorache has more than 9 years of experience with ontology
> development
> > and Semantic Web technologies. She is also one of the key team member of
> > the Prot?g? team. As a research scientist, Dr. Tudorache has done
> extensive
> > work on the collaborative development of large biomedical terminologies
> and
> > ontologies. She has also designed and implemented the initial versions of
> > WebProt?g? ? a light-weight ontology and knowledge base editor for the
> Web.
> > She is the lead person of the team developing the ICD Collaborative
> > Authoring Tool (iCAT) - an adaptation of WebProt?g? that the World Heath
> > Organization is currently using to build the 11th revision of the
> > International Classification of Diseases. Dr. Tudorache has organized and
> > chaired several international Semantic Web conferences, and has served
> as a
> > program committee member on numerous occasions.
> >
> > Matthew Horridge is a research software developer in the Biomedical
> > Informatics Research Group at Stanford University. He works on the
> Prot?g?
> > project, developing front and back end components for both WebProt?g? and
> > Prot?g? 4.  In addition to this, Matthew has worked extensively on the
> > design and implementation of the OWL API, which is the most popular API
> for
> > dealing with OWL ontologies and underpins the latest versions of
> WebProt?g?
> > and Prot?g? 4.  His research interests centre around the explanation of
> > entailments in ontologies and he recently received a PhD from the
> > University of Manchester in this area.
> >
> >
> > WEBEX DETAILS:
> > -------------------------------------------------------
> > To start or join the online meeting
> > -------------------------------------------------------
> > Go to
> >
> >
> https://stanford.webex.com/stanford/j.php?ED=205918092&UID=481527042&PW=NMmEyZWM0YTg1&RT=MiM0
> >
> > Meeting Number: 923 724 964
> > Meeting Password: ncbo
> >
> >
> > -------------------------------------------------------
> > Audio conference information
> > -------------------------------------------------------
> > To receive a call back, provide your phone number when you join the
> > meeting, or call the number below and enter the access code.
> >
> > Call-in toll number (US/Canada): 1-650-429-3300
> >
> > Global call-in numbers:
> >
> >
> https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=205918092&tollFree=0
> >
> >
> > Access code:923 724 964
> >
> >
> >
> > Trish Whetzel, PhD
> > Outreach Coordinator
> > The National Center for Biomedical Ontology
> > Ph: 650-721-2378
> > http://www.bioontology.org
> >
> > "Like" NCBO on Facebook: http://on.fb.me/bioontology
> >
> > Follow NCBO on Twitter: http://twitter.com/#!/bioontology
> >
> > Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
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> >
> > ------------------------------
> >
> > _______________________________________________
> > protege-discussion mailing list
> > protege-discussion at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> >
> >
> > End of protege-discussion Digest, Vol 75, Issue 10
> > **************************************************
> >
>
>
>
> --
> *Warm Regards
> Ganesh Kumar S
> 0064212388360
> *
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 09 Oct 2012 18:05:26 -0700
> From: Timothy Redmond <tredmond at stanford.edu>
> To: protege-discussion at lists.stanford.edu
> Subject: Re: [protege-discussion] protege-discussion Digest, Vol 75,
>         Issue 10
> Message-ID: <5074C9D6.5090006 at stanford.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
>
> The easiest method is to copy the pprj file for the database project to
> the other location.  The pprj project contains all the needed
> information to connect to the database project.  The only issue might be
> if you have used localhost to access the database and this hostname does
> not work from the other location.
>
> Failing that, you can connect directly to the database project from
> Protege using the new project menu (perhaps not too intuitive).  Do the
> following:
>
>  1. In the "Welcome to Protege" (or in the File menu) select new project.
>  2. **Very important** - make sure that the "Create from existing
>     sources" is checked.
>  3. Choose either OWL/RDF database or Protege database depending on
>     whether your project is an OWL database project.
>  4. (Assuming you chose OWL/RDF) choose OWL Database in the next window.
>  5. Then you get a window where you can enter your configuration
> parameters.
>
> -Timothy
>
>
>
> On 10/09/2012 05:03 PM, Ganesh kumar wrote:
> > Hi Timothy,
> >
> > Thanks for your response.
> > I have decided to use mysql as my backend.
> >
> > I have a new question like - After I create a new database project, I
> > need to open the same project from another location.
> > But in Open project menu, I do not see an option to open a project
> > from database.
> >
> > Can you please help me to resolve this issue
> >
> > Thanks in advance.
> >
>
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
>
> End of protege-discussion Digest, Vol 75, Issue 11
> **************************************************
>



-- 
*Warm Regards
Ganesh Kumar S
0064212388360
*
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