I ve tried to load uberon ontology to R using onctoCAT package, but it drops an error I do not really understand, because the URI seems to be valid to me. I have also tried to load the ontology from the local files (both .obo and .owl), but the resul was in all cases the same. Protege was able to load the ontology (at least in .owl format).
>uberon_onto <- getOntology('http://berkeleybop.org/ontologies/uberon.owl') WARN [ReasonedFileOntologyService] The inverse object property contained_in for contains was not found in the ontology Sorry, can't create Ontology object. Please, check ontology's URI: http://berkeleybop.org/ontologies/uberon.owl.
However, I was able to load some other ontologies like gene ontology or development anatomy ontology (http://www.berkeleybop.org/ontologies/obo-all/human-dev-anat-abstract2/human-dev-anat-abstract2.obo). I found related question ontoCAT getEFO error but the problem seems to be different since my version of R is > 3.2.
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  gplots_2.17.0 BiocInstaller_1.20.0 ontoCAT_1.22.0 rJava_0.9-7 loaded via a namespace (and not attached):  tools_3.2.2 KernSmooth_2.23-15 gdata_2.17.0 caTools_1.17.1 bitops_1.0-6 gtools_3.5.0
Thanks in advance.