[BioSQL-l] PhyloDB module updates

[Hilmar Lapp]

On Feb 14, 2008, at 7:56 PM, Peter wrote:

> On Thu, Feb 14, 2008 at 3:11 AM, Hilmar Lapp <hlapp at gmx.net> wrote:
>> Hi all,
>>
>>  I am proposing the following schema updates to the PhyloDB module.
>>  Though I have committed these already, PhyloDB is pre-alpha and  
>> still
>>  quite heavily evolving, so changes can be made relatively easily.
>>  ...
>
> I may be showing my ignorance here, but how does this affect the
> existing taxon ID tables in BioSQL? Or will it replace them?


It doesn't. The taxon (and taxon_name) tables are in the core schema,  
not in the phyloDB module.

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.

However, there is no guarantee that a phylogenetic tree refers only  
to taxa that are also in the NCBI taxonomy, so in the long inaction  
also isn't really an option.

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