Closed GoogleCodeExporter closed 9 years ago
Hello and thank you for reporting the issue.
I can reproduce the error, but after investigating the issue, I can't offer a
quick solution.
The problem is that you want to use the same ontology for query and load.
During the load this leads to an internal error (OWLAPI ontology already
exists, which has a null error message, grr)
But as you might have already tested, you can't just skip one of the files. I'm
not sure when we are able to work on this issue.
Maybe you can provide more input on what the use-case is you are trying to
solve.
Depending on what you want to create, OORT might not be the correct tool to
use. The command-line OWTools (although a beast of its own) might be a better
alternative.
Original comment by HDie...@lbl.gov
on 13 Nov 2014 at 9:32
Thanks for the reply!
Are there any "Windows" command-line OWTools?
this is what I'd like to do:
https://code.google.com/p/owltools/wiki/OortExtractingModules
Extract a class and all its subclasses and create an owl ontology from it.
Is that possible?
Maybe I should try owltools on a Linux VM?
Paty
Original comment by 4pa...@gmail.com
on 13 Nov 2014 at 9:48
> Are there any "Windows" command-line OWTools?
No, not specifically. But it is not that hard to get OWLTools running on Windows
The wrapper script is written for a Linux/Unix like environment, but it just
assembles the relevant details for memory setting and other setup details.
Using a VM might be a bit of an overkill for that.
You can download the required jar for owltools here:
http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar
In theory you just can to run that jar using Java:
java -Xmx2048M -jar owltools-runner-all.jar
> Extract a class and all its subclasses and create an owl ontology from it.
Definitely possible (OORT is not the recommended tool for that)
The relevant owltools option is '--extract-module' to extract an ontology
modules for a given set of classes. Using the sub option '-d' (for deepening)
will retrieve all subclasses of the initial set before extracting the module.
Using '--elk' flag will use the efficient elk reasoner to retrieve the
subclasses
So in total the command could be:
java -Xmx4G -jar owltools-runner-all.jar --elk cl.owl --extract-module -d
http://purl.obolibrary.org/obo/CL_0000202 -o cl-module.owl
Original comment by HDie...@lbl.gov
on 13 Nov 2014 at 10:14
Hello,
is there any more input required for the issue? Did the work around using
owltools help?
Original comment by HDie...@lbl.gov
on 21 Nov 2014 at 7:03
As no further input from the original requester is available, assume the
problem has been resolved with the provided work-around.
Original comment by HDie...@lbl.gov
on 4 Dec 2014 at 9:56
Original issue reported on code.google.com by
4pa...@gmail.com
on 13 Nov 2014 at 7:34Attachments: