Datasets:
D3FEND
Branch: https://github.com/d3fend/d3fend-ontology/tree/release/0.13.0-BETA-1
Commit: 3dcc495879bb62cee5c4109e9b784dd4a2de3c9d
CWE extension: https://github.com/d3fend/d3fend-ontology/tree/release/0.13.0-BETA-1/extensions/cwe
After building d3fend-full.owl I imported the ontology into Protege version 5.6.1 with the Pellet reasoner plug-in. First I use the Debug Ontology plugin to check the ontology for consistency and coherency. If it all checks out, I move onto exporting the inferences.
In Protege navigate to File>Export Inferred Axioms as ontology and make sure to check all of the checkboxes including asserted axioms and annotations. See this blog post for more information: https://www.michaeldebellis.com/post/export-inferred-axioms.
Once you have the materialized ontology you can filter it with d3fend.sparql.
arq --query=d3fend.rq --data=d3fend.owl --results=turtle > d3fend.ttl
riot --output=nt d3fend.ttl > d3fend.nt
The d3fend.owl and d3fend.nt files then are compressed using gzip.