Paper long abstract:

First proposed around 1993, the ontology has taken the database world by storm. In that year, Thomas Gruber, an informational scientist, wrote: "The term [ontology] is borrowed from philosophy, where an ontology is a systematic account of Existence". Informational scientists were quick to adopt the term and the idea: an ontology is a vocabulary wedded to formal logic. Outsiders raised eyebrows. Why use a word with such a heavy load of philosophical connotations? Yet, the term is surprisingly apt. It goes straightforwardly "back to Aristotle" and after a short while, the term received the approval of professional philosophers, such as Barry Smith who in 2002 launched the Basic Formal Ontology Project, with many applications in the neurosciences and other biomedical sciences. Smith's background is in Aristotelian realism, combined with analytical philosophy.

From a conceptual point of view, the ontology has obvious advantages for users (i.e. "domain scientists"), yet one would expect that it also has important limitations. In principle, domain scientists might become enabled to revise existing structures of ontologies. Yet, in many cases, scientists suspect that curators will control ontologies. A particular taxonomic logic would structure the theoretical and experimental practices in the sciences. Will non-ontological structures for databases be a way out for scientists? I suspect their possibility on the basis of the existence of various "paradigms" within taxonomy: the deductive-hierarchical, the intuitive-pragmatic, the baroque and the typological approaches to taxonomy.