The word ontology literally means ``a branch of metaphysics relating to the nature and relations of being.'' Our use of the word is much more restrictive, dealing only with the nature of, and relationships among, concepts within a narrow subject area. Attempts to specify ontologies for scientific disciplines are very common, with most disciplines having some kind of subject classification scheme by this time. However, as Lakoff points out,[Lak87], ``human categorization is based on principles that extend far beyond those envisioned in the classical theory.'' As a result, simple classification methods leading to taxonomies of concepts are inadequate for expressing the rich variety of human categorization techniques.
The KEYNET system depends on having a background ontology that defines the structure and behavior of keynets. The Ontology Builder[BF93] is a system related to KEYNET that provides support for constructing and maintaining subject-specific ontologies that have much richer semantics than simple taxonomies.
One of the important features of the Ontology Builder is that it will automatically generate tools for entering keynets. We currently have a prototype called the M&M-Query system that has such a tool specialized for entering knowledge frames for the Materials &Methods sections of biological research papers[BF93]. This prototype furnished an important ``proof of concept'' for the feasibility of using such tools for annotating documents.