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In 11g you could load an ontology (in n-triple form) using the bulk loader which involves first using SQL*Loader to loada the data into a table, and then invoking a bulk loader from a SQL prompt. In 10g you can use a batch loader, which is a command-line java interface. The batch loader is available in later patches of 10.2. 11g has batch loader support as well.
Additionally for very small ontologies you might find using SQL INSERT statements useful.
All this is documented in Oracle® Database Semantic Technologies Developer's Guide 11g Release 1 (11.1).
Can you give more detail about the example using Protege to import an OWL ontology directly to Oracle11g?