[BioSQL-l] class taxon_name and genbank

[Peter]

On Fri, Oct 3, 2008 at 11:50 AM, Raoul Jean Pierre Bonnal
<raoul.bonnal at itb.cnr.it> wrote:
> Dear all,
> accession AB030700
>
> SOURCE      Rattus norvegicus (Norway rat)
>  ORGANISM  Rattus norvegicus (Norway rat)
>
> looking into taxon_name I can find only:
>
> Rattus norvegicus
>
> where did you store "(Norway rat)" ?
> NCBI identify "(Norway rat)" as
>
> "Genbank common name: Norway rat"

Hi Ra,

How did you load this GenBank file into BioSQL?  My guess is with
BioPerl.  Also, did you pre-load the NCBI taxonomy using the BioSQL
script load_ncbi_taxonomy.pl?  This will probably have an impact too.

In any case, I suggest you look at the taxon and taxon_name tables in
BioSQL.  This can store the scientific name plus the common name.  I
would expect both "Rattus norvegicus" and "Norway rat" to be there for
your entry, but without known more of the specifics its hard to guess.

Peter