One difference - Faceted Navigation:
Data in the enterprise often has more meta data, and can therefore allow users to drill down into search results; some vendors call this parametric search. We're talked about these terms in previous articles.via Enterprise Search Blog
If the docs lack meta data, but are at least organized in some type of overall logical order, then a taxonomy might work.
If the content is completely unstructured, a sometimes-acceptable alternative is to use unsupervised clustering, but we usually view this as a workaround – if you have good meta data (or database fields), or at least some type of overall rule-based organization, faceted / parametric navigators or taxonomies will usually give more pleasing results.
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