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The organism hierarchy uses international taxonomic names to a large extent, which can be found in the Editorial Guide. Where this is not in contradiction with national language policies, the names of organisms should be retained as universal (international) scientific terms and should be consistent with existing spelling rules, in particular as regards capitalization of terms (e.g. “Chlamydia pneumoniae”, “Spirochaete dentium”, “Dependovirus”, etc.; it is important to note that the current version of SNOMED CT may contain incorrect lower case letters.)

The Organism hierarchy has no relation types with which to specify properties. As a result, it contains instead a large number of grouper concepts such as “gram-negative bacterium”. In English, groupers are represented by the common names "infectious agents" or "arthropod organisms". If a common name is used in English, it is recommended to use a common name in the target language as well.  Most organism concepts correspond to a taxonomic entry in the Linnaean taxonomy, but some, such as gram-negative bacteria, have only a common name. In that case, you should translate to a common name in the target language.

SNOMED CT also tends to lag behind the very fast developments in the micro-organism thesauri. It contains many obsolete names as separate concepts, which have become synonymous with another concept. Such issues are quickly resolved when pointed out. The Editorial Guide lists specific resources for bacteria, viruses, parasites, and so forth (