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How to reference the NCBI taxonomy database

The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.

However, if you want to acknowledge the fact that you have used the NCBI taxonomy database and other NCBI services and databases for your research, the two following papers can be referenced:

1. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
   Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
   Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
   Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
   Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
   Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
   of the National Center for Biotechnology Information. Nucleic Acids
   Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21. [PubMed]

2. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
   GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
   Epub 2008 Oct 21. [PubMed]