[BioSQL-l] NCBI Taxonomy

[Peter Cock]

On Wed, Jan 15, 2014 at 7:09 AM, Trevor Bell <trevorgrahambell at gmail.com> wrote:
> I have worked through the BioSQL tutorial
> (http://biopython.org/wiki/BioSQL) successfully. I am now interested
> in importing sequences from one organism only, which I am interested
> in. Do I need the NCBI taxonomy? It's a very large amount of data,
> almost all of which will not be used or relevant? Please advise.
>
> Thanks.

Hi Trevor,

You can perhaps skip it, but you may find this means
the organism names are effectively lost on import.
The details will depend on which bindings you are
using - Biopython can query NCBI Entrez to fetch
the specific bits of the NCBI taxonomy needed, giving
a gradual/incremental population of the taxonomy
tables.

Peter