[BioSQL-l] NCBI Taxonomy

[Trevor Bell]

Thanks for the reply. I created another test case using the tutorial as
before, but did not include the steps to import the NCBI Taxonomy. It
worked successfully, and the TAXON table contains the name of the organism
from the single sequence I added.



On 15 January 2014 10:02, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 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
>



-- 
Dr Trevor G. Bell
BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD