[kepler-users] Adding my own ontology to the Kepler 2.3 semantic types

[Michael.O'Connor at csiro.au]

Hi again,

I have experimented with the various suggestions and help.

On my Kepler install (2.3 running on OS X 10.7.3) I found
— the Tagging module had to be installed before additions to ontology_catalog.xml were read.
— once Kepler encounters an unreadable (or incompatible) .owl file it doesn't read any further in ontology_catalog.xml
— Editable (from within Kepler) ontologies have to be created inside Kepler using the Tagging module.
— added ontologies seem to need LSID for one or both of xmlns= and xml:base= . Not sure if it's needed at owl:Ontology rdf:about= too.

I would be grateful for yay/nay on whether these findings are correct. Also, on the last point — what makes for an ontology file that is compatible with Kepler?  (Prior to using Kepler my ontology had a temporary IRI (for use in development on a local machine) of http://purl.csiro.au/ROBE/ROBE-core.owl) Perhaps I can't keep that if I want to annotate Kepler objects with my ontology.

- Mike

From: Sean Riddle <swriddle at gmail.com<mailto:swriddle at gmail.com>>
To: Shawn Bowers <bowers at gonzaga.edu<mailto:bowers at gonzaga.edu>>
Cc: "O'Connor, Mike (CES, Floreat)" <Michael.O'Connor at csiro.au<mailto:Michael.O'Connor at csiro.au>>, "kepler-users at kepler-project.org<mailto:kepler-users at kepler-project.org>" <kepler-users at kepler-project.org<mailto:kepler-users at kepler-project.org>>
Subject: Re: [kepler-users] Adding my own ontology to the Kepler 2.3 semantic types

Yes, there is. That's just a GUI to edit ontology_catalog.xml, though, I think.

- Sean

On Thu, Apr 26, 2012 at 2:28 PM, Shawn Bowers <bowers at gonzaga.edu<mailto:bowers at gonzaga.edu>> wrote:
Hi,

If I recall correctly, I thought there was also a way to "register" an
ontology via the tag editor (not sure what this is called)? I know
this was in an initial version of the tagging module.  I don't have it
up and running here to check ...

Shawn

On Thu, Apr 26, 2012 at 2:23 PM, Sean Riddle <swriddle at gmail.com<mailto:swriddle at gmail.com>> wrote:
> If I recall, the ontology_catalog.xml file you edited is copied into place
> in the ~/.kepler directory if it is not already there. Adding your edit to
> the copy in .kepler (or just deleting the copy in .kepler, which should
> re-copy your modified version) should get you up and running.
>
> Also, I would try using absolute paths to your ontologies first and then
> experimenting to determine with respect to what local pathnames are
> calculated (probably the main Kepler directory).
>
> - Sean
>
> On Thu, Apr 26, 2012 at 5:13 AM, <Michael.O'Connor at csiro.au<mailto:Michael.O'Connor at csiro.au>> wrote:
>>
>> I wanted to add my own ontology to Kepler, so that I could semantically
>> annotate inputs and outputs in my workflows.
>>
>> I have found at least one message in the kepler-user lists that discusses
>> this:
>>
>>  http://lists.nceas.ucsb.edu/ecoinformatics/pipermail/kepler-users/2006-January/000053.html
>>
>> Followed the suggestions by:
>> — adding my .owl file to
>> /Applications/Kepler-2.3/Kepler.app/Contents/Resources/Java/common-2.3.0/configs/ptolemy/configs/kepler/ontologies
>> — in the same folder I added an entry to ontology_catalog.xml i.e.
>> <ontology filename="myOwl.owl" library="false"/>
>>
>> My ontology did not appear in the list of Categories in the Input tab of
>> the Semantic Type Annotation dialog.
>>
>> Next approach — my ontology might not be correctly formed as far as Kepler
>> is concerned (it does open fine in Protege 4.2)?  So I made a copy of one of
>> the SEEK ontologies and tried that, as above, but the same lack of result.
>>
>> Perhaps I'm putting the ontology in the wrong place (i.e. not inside the
>> folder for the Application) or I have to rebuild or compile something to get
>> this to work.
>>
>> Any help gratefully received,
>>
>> — Mike
>> _______________________________________________
>> Kepler-users mailing list
>> Kepler-users at kepler-project.org<mailto:Kepler-users at kepler-project.org>
>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>
>
>
> _______________________________________________
> Kepler-users mailing list
> Kepler-users at kepler-project.org<mailto:Kepler-users at kepler-project.org>
> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>