[BioSQL-l] The taxon table

[Hilmar Lapp]

> -----Original Message-----
> From: Yves Bastide [mailto:Yves.Bastide at irisa.fr] 
> Sent: Tuesday, July 01, 2003 1:01 AM
> > 
> > Also 
> is taxonomy optional in BioSQL or will any fresh install of 
> > BioSQL need to load the ncbi taxonomy data by default ?
> 
> The taxonomy is optional; furthermore, species can be added at will 
> using e.g. biosql-pg's persistence.
> 

Correct. I do recommend though to pre-load the taxonomy database, as
species designations are a challenge to parse generically under every
circumstance. If you have a NCBI taxon ID provided in the datasource,
and most public datasources do provide that, you can reduce the problem
of getting the species correct to making a look-up by NCBI taxon ID.

That also means that every library establishing persistence to biosql
should look up species by taxon ID first, not species name. If the taxon
is actually an E.coli strain but the full binomial for some reason
doesn't include the strain name properly, you'll end up linking to the
wrong taxon if you look up by 'E. coli'.

	-hilmar

> > 
> > cheers
> > 
> > _greg
> > 
> yves
> 
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