It appears than taxonomy and ontology are not quite the same but they do have a common base. At a SemTech conference the consensus seems to have been that, "Taxonomists build hierarchies, and ontologists determine classes or categories."
Author goes on to describe the use of class (or facet) analysis.
"Defining classes or ontology work typically precedes building the taxonomy. Defining the classes is like writing a specification for the taxonomy; in fact defining classes is the same as defining facets. The goal of a taxonomist and ontologies should be to define a specific, unambiguous description of a term that helps manage how we find and organize content so the pathways are clear and specific; adding an ontology ensures that the term is placed in the most specific categories to help ensure clarity and lack of ambiguity."
Modelling strategies are needed to do this well. Posting mentions some tools and approaches.
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