[BioSQL-l] class taxon_name and genbank

[Hilmar Lapp]

Hi Raoul,

the BioSQL taxonomy tables are modeled directly based on the NCBI  
taxonomy model, which has nodes, each of which represents a taxon  
(where a tip, e.g., species, or an internal node, e.g. family), and  
one or more names for each node. The name_class column in taxon_name  
gives the type of the name.

NCBI uses 'scientific name' as the name_class for the currently valid  
latin name (binomial). 'Norway rat' would have name_class 'common  
name'. There are others, such as misspellings etc.

If you use the load_ncbi_taxonomy.pl script that comes with BioSQL,  
that's how the taxonomy will be loaded.

Does this answer your question?

	-hilmar

On Oct 3, 2008, at 6:50 AM, Raoul Jean Pierre Bonnal 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"
>
>
> --
> Ra
>
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> BioSQL-l at lists.open-bio.org
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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