[Bioperl-l] Bio::*Taxonomy* changes

Sendu Bala bix at sendu.me.uk
Wed Jul 26 16:25:41 UTC 2006

Hilmar Lapp wrote:
> On Jul 26, 2006, at 5:19 AM, Sendu Bala wrote:
>>>> It seems like the main problem with Node right now is that it has
>>>> classification() and things like genus(). I propose pure Node method
>>>> solutions to answer the questions classification() and genus() were
>>>> implemented to answer, but in a better, cruft-free way.
>>>> Bio::DB::Taxonomy::genbank anyone?
> Sorry, can you summarize this in a few sentences? If you do want 
> feedback from me you really need to be more concise.

A bad solution-module stores any kind of taxonomic information outside 
of the solution-module or in an inconsistent form. By 'inconsistent' I 
mean, sometimes you store the name of a taxonomic rank with 
$node->node_name, other times you store it in an array or scalar held 
directly on the solution-module or elsewhere.

Bio::Taxonomy specifically is not usable. Generally speaking, classes 
that are containers of multiple nodes are also inappropriate, because 
they result in excess database retrieval and excess storage of 
duplicated information amongst instances of such classes.

Bio::Taxonomy::Node combined with Bio::DB::Taxonomy::list would probably 
be ideal.

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