[BioSQL-l] PhyloDB module updates

[Hilmar Lapp]

On Feb 14, 2008, at 8:26 AM, Chris Fields wrote:

>
> On Feb 14, 2008, at 5:17 AM, Hilmar Lapp wrote:
>
>>
>> [...]
>> Though speaking of which, what has been bugging me lately is that  
>> they only provide for a single taxonomy to be used (presumably the  
>> one from NCBI, since one column expressly refer to the  
>> NCBI_taxon_ID. I've been thinking about suggesting to generalize  
>> that a little, but the backwards compatibility issues might just  
>> outweigh the benefits.
>> [...]
>>
> I think it would be better to generalize it within the schema.  Is  
> there a way to indicate what taxonomy was used (NCBI, custom, etc)?

Not at present, it is the NCBI Taxonomy by convention (and as that is  
what GenBank/DDBJ/EMBL sequences will refer to).

To represent that, the taxon table would in essence need to receive a  
foreign key to biodatabase to indicate the namespace (which would be  
NCBI Taxonomy by default), and to allow for multiple taxonomies (each  
in a different namespace).

(Generalizing the NCBI_Taxon_ID column is easy - it would just be a  
generic Identifier.)

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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