How are organisms in the NCBI Taxonomy database formally named?

The NCBI Taxonomy follows three Codes of Nomenclature plus a set of recommendations for viruses:

• International Code of Nomenclature of Prokaryotes (ICSP) for prokaryotes
• International Code of Zoological Nomenclature (ICZN) for animals and others
• International Code of Nomenclature (ICN) for plants, algae and fungi (published as a book)
• Viruses do not have a code of nomenclature, but scientists follow recommendations from the International Committee on Taxonomy of Viruses (ICTV).

In all cases the Taxonomy staff try to indicate and apply valid names which means, a scientific name that was designated according to the rules of its relevant Code of Nomenclature. Names that do not correctly follow these rules have different designations such as effective, illegitimate, invalid or superfluous. The Codes differ in how these terms are applied and defined, meaning that different groups of organisms require different rules and terminology according to their Code.

For a deeper insight check, for example, the conditions for a prokaryote name to be valid:

• follow the rules of its relevant code (ICSP)
• One of these:
  1. Was included in the 1980 Approved Lists of Bacterial Names
  2. Has been published more recently in an issue of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) or the same journal published under one of its earlier titles
  3. Has been published in a different publication but was subsequently included in a Validation List published in an issue of the IJSEM (example)

If a prokaryote name has been published following the rules of its relevant Code but has not (yet) met any of the three other criteria above, it is said to be effectively (but not yet validly) published. It can subsequently be made valid by following step 3. above. In bacteriology, effectively published names are indicated as such by including the taxonomic name in double quotes. Note also that the validity of a taxonomic name (nomenclature) is unrelated to its classification. It’s a legalistic term that means that the taxonomic name has been created in accordance with the rules of nomenclature for the particular Code under which it falls.
For example, Domibacillus aminovorans was effectively but not validly published because the name was not included in the 1980 Lists of Approved Names. Coincidentally, (but a separate issue) this taxon used to be misclassified as Bacillus aminovorans.