The method of facet-based searching of databases uses a facet ranking scheme for the searching and information retrieval from large scale, semantic databases, such as semantic biological databases. The method of facet-based searching of databases includes a ranking scheme for facet values to order them by their significance to a search query. The method of facet-based searching of databases also includes a subsequent scheme to present the user with a narrowed set of facet values when a large number of choices are available. In biological databases, for example, users are typically interested in finding average or extreme values. Thus, the user is able to narrow the set of facet values to values that are average, most common, least common and/or most/least significant in a search result. Additionally, the facets themselves can be ordered according to their usefulness in narrowing down the search.