Looking for a file : Complete Ref Seq Systematic Classification

Question

[Rox]

Hello Biostar,

I'm sorry if this is an innapropriate place to ask for it, but I can't find this file by myself and actually don't know if it exist. I'm looking for a file containing the whole systematic classification of RefSeq, I have a table that would look like this in mind :

https://www.encyclopedia.com/reference/encyclopedias-almanacs-transcripts-and-maps/examples-systematic-classification-table

I mostly need the "species name" (latin) associated with the "class". does anyone know if such a file exist and where I could find it ?

Cheers,

Roxane

[Benn]

I am not completely sure what you mean by "systematic classification of RefSeq". RefSeq is on gene/protein annotation level. Do you want all species in RefSeq? Or do you mean you want taxonomic data as in https://www.ncbi.nlm.nih.gov/taxonomy/?

Please explain what you want to do with it, so we can understand what you need.

Answer 1

[Sej Modha]

You can find this information in the NCBI taxonomy files that can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump. Please see readme file for more info: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/taxdump_readme.txt

rankedlineage.dmp contains following columns.

rankedlineage.dmp
-----------------
Select ancestor names for well-established taxonomic ranks (species, genus, family, order, class, phylum, kingdom, superkingdom) file fields:

    tax_id                  -- node id
    tax_name                -- scientific name of the organism
    species                 -- name of a species (coincide with organism name for species-level nodes)
    genus                   -- genus name when available
    family                  -- family name when available
    order                   -- order name when available
    class                   -- class name when available
    phylum                  -- phylum name when available
    kingdom                 -- kingdom name when available
    superkingdom                -- superkingdom (domain) name when available

[Rox]

Thanks a lot that was exactly what I was looking for ! Have a nice day :)