Have you ever been confused by multiple taxonomic names for a single organism? You’re not alone! It’s one of the challenges in maintaining any biological database. Recently we updated the NCBI TaxBrowser to assist with this.
Let’s start with a brief word about how investigators name species in the first place. For any new species, the reporting author declares a “type.” They then deposit a specimen, or “type material,” in a publicly available biorepository. This type material is tied to the new species name and serves as a reference for future comparisons. Researchers can then use DNA sequences obtained from type material to identify other samples from the same species. NCBI currently uses such an approach to verify the taxonomic assignment of prokaryotic genomes.
Our Taxonomy group has been curating type material records in the Taxonomy database since 2013 using a common vocabulary accepted by our international partners (the INSDC). For example, the Entrez query “type material[prop]” in the Taxonomy database will return all type material at NCBI.
So what are the improvements to the TaxBrowser?
Figure 1 shows the TaxBrowser view for taxid 27304, a yeast described from brined cucumbers in 1950 as Brettanomyces versatilis. The updated page shows this basionym (original name) beneath the current name, Wickerhamiella versatilis. The page also lists the name Debaryomyces tamarii as a heterotypic synonym, since more recent data clarified that it refers to the same species. The page also provides links to the literature where these names were originally declared, as well as to the biorepository in the NCBI BioCollections database and the specimen/culture page at that institution. The “Entrez records” table contains a new column (“Links from type”) that provides links to type material records in the Nucleotide, BioSample and Assembly databases. Previously, you would have needed a diverse set of Entrez search terms to find these records.
We hope these improvements will help reduce taxonomic confusion. Why not try this out with your favorite species and let us know what you think!
For further reading:
- Federhen, S. (2012) The NCBI Taxonomy database. Nucleic Acids Research, 40, D136-D143.
- Federhen, S. (2015) Type material in the NCBI Taxonomy Database. Nucleic Acids Research, 43, D1086-D1098.
- Karsch-Mizrachi, I., Takagi, T., Cochrane, G. (2018) The international nucleotide sequence database collaboration. Nucleic Acids Res, 46, D48-D51.
- Ciufo, S., Kannan, S., Sharma, S., et al. (2018) Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol, 68, 2386-2392.
- Sharma, S., Ciufo, S., Starchenko, E., et al. (2018) The NCBI BioCollections Database. Database : the journal of biological databases and curation, 2018, bay006.