The semantic annotations are stored according to the protonkm.owl ontology in <KIM_HOME>/ontext/default/kb/owl/. Generally, all RDF in Sesame can be accessed via the SemanticRepositoryAPI. The DocumentRepositoryAPI provides an object-oriented access to the stored documents.
Only annotations with "inst" and "class" features are considered semantic annotations and only they are stored. The default KIM pipeline produces only semantic annotations.