Vocabularies and retrieval tools in biomedicine: disentangling the terminological knot

Terms like "thesaurus", "taxonomy", "classification", "glossary", "ontology" and "controlled vocabulary" can be used in diverse contexts, causing confusion and vagueness about their denotation. Is a thesaurus a tool to enrich a writer's style or an indexing tool used in bibliographic retrieval? Or can it be both? A literature study was to clear the confusion, but rather than giving us consensus definitions, it provided us with conflicting descriptions. We classified these definitions into three domains: linguistics, knowledge management and bibliographic retrieval. The scope of the terms is therefore highly dependent on the context. We propose one definition per term, per context. In addition to this intra-conceptual confusion, there is also inter-conceptual vagueness. This leads to the introduction of misnomers, like "ontology" in the Gene Ontology. We examined some important (bio)medical systems for their compatibility with the definitions proposed in the first part of this paper. To conclude, an overview of these systems and their classification into the three domains is given.