An annoying thing that keeps occurring while I’m trying to update phage metadata is that I’m heavily relying on NCBI:Taxonomy. Well, obviously I know I can’t blame them since they post a not-so-funny disclaimer at the end of any record

Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification – please consult the relevant scientific literature for the most reliable information.

However, it is really annoying and it reflects everything else in NCBI: so static, unlike everything else on the web in the past 5 years… Now to update the record of each of about 55 phages described as “unclassified” in NCBI, I have to spend anything between 10 – 100 minutes, and I may end up without getting an answer. Just take for example, Gifsy-1 and Gifsy-2, two of the most famous prophages of Salmonella. They are lambdoid phages, i.e. tailed siphoviruses. Yet, their NCBI records say: unclassified!

ICTV doesn’t seem to be doing any better with individual viruses (see their latest list).

This is not why I started this post anyway, I’m trying to document the “evidence” behind my taxonomy udpates to the metadata table, because it would be too messy if I include these data in each cell of the Google Doc. However, maybe later we will come up with a ‘taxonomy evidence’ record as we have an annotation evidence one in the SEED database (called ‘Feature evidence’).

Metadata evidence:

• Gifsy: from Salmonella: Methods and Protocols @ Google Books
• Enterobacteria phage YYZ-2008: This one is tricky. BLASTN shows that its best matches are Enterobacteria phage 2851 (classified as Podoviridae) and Stx2-converting phage 1717 (classified as Siphoviridae)