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 <[email protected]<mailto:[email protected]>> To: Shawn Bowers <[email protected]<mailto:[email protected]>> Cc: "O'Connor, Mike (CES, Floreat)" <Michael.O'[email protected]<mailto:Michael.O'[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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'[email protected]<mailto:Michael.O'[email protected]>> 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 >> [email protected]<mailto:[email protected]> >> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users > > > > _______________________________________________ > Kepler-users mailing list > [email protected]<mailto:[email protected]> > http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users > _______________________________________________ Kepler-users mailing list [email protected] http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
