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. 2015 Jan;43(Database issue):D1086-98.
doi: 10.1093/nar/gku1127. Epub 2014 Nov 14.

Type material in the NCBI Taxonomy Database

Scott Federhen  1
Affiliations

Type material in the NCBI Taxonomy Database

Scott Federhen. Nucleic Acids Res. 2015 Jan.

Abstract

Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species. For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria. The NCBI Taxonomy Database (http://www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes. This has important implications for many NCBI resources, some of which are outlined below.

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Figures

Figure 1.
Figure 1.
Correctly identified but taxonomically misplaced species, in need of a formal taxonomic revision.
Figure 2.
Figure 2.
Taxonomic distribution of sequence from type. Taken from the Tree view of the interactive taxonomy portlet on the sidebar of Nucleotide Entrez. (a) All type material. (b) Type material from eukaryotes other than fungi. (c) Type material from the animals.
Figure 3.
Figure 3.
Sequence from type in Cercopithecus lomamiensis. Clockwise from top: (1) taxonomy entry for Cercopithecus lomamiensis. (2) GenBank flatfile format for accession JN106060. (3) Holotype specimen page at the Yale Peabody Museum, Mammal Collection.
Figure 4.
Figure 4.
(a) Type genomes in the Dickeya clade of the k-mer tree. (b) Proxytype genomes for Raoultella ornithinolytica and Klebsiella oxytoca in the k-mer tree. (1) Best proxytype candidate genomes for Raoultella ornithinolytica, including one submitted as Klebsiella oxytoca and two misidentified as Escherichia coli. (2) Best proxytype candidate genomes for Klebsiella oxytoca. (3) Best BLAST hit for AB008147, submitted as type sequence from Klebsiella oxytoca.
See this image and copyright information in PMC

References

    1. Federhen S. The NCBI Taxonomy Database. Nucleic Acids Res. 2012;40:D13–D25. - PMC - PubMed
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