Clips, Jess, JessTab Ontology Extractor (CJJTOE) was the second tool I have built. In a nutshell, CJJTOE extracts the classes and their slots referred to in a set of Clips, Jess and JessTab rules and, using the Protege API, builds the corresponding ontology. It attempts to infer the taxonomic structure of the classes based on superclass-subclass inheritance of attributes. The inferred taxonomy is saved as a Protege project, allowing it to be manipulated like any other ontology developed in Protege.
The tool is available to download, currently it runs as a standalone Java application, the instruction manual describes how to install and run it.
There is a video showing how CJJTOE extracts an ontology from some Jess code which defines a series of deftemplates modelling aspects of the newspaper ontology. Be warned: the video is quite large (about 24MB). You can also get the news.clp file used in the demo.