[BioSQL-l] PhyloDB module updates

[Chris Fields]

On Feb 14, 2008, at 5:17 AM, Hilmar Lapp wrote:

>
> 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
> -- 

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)?

chris