[Bioperl-l] Bio::Species/Bio::Taxonomy changes

[Chris Fields]

On Jul 23, 2006, at 7:58 PM, Hilmar Lapp wrote:

>
> On Jul 23, 2006, at 4:53 PM, Chris Fields wrote:
>
>> I also propose (I'll probably get yelled at here) NOT actively
>> supporting additional parsing of species, subspecies, etc directly
>> from a file w/o a DB lookup.  As in, leave species, subspecies, genus
>> parsing from the flatfile as is (no longer support it) or remove it
>> completely and leave them unset.
>
> Note that most (as in: most used, not most taxa) cases are actually  
> straightforward. I don't think removing what's there is desirable,  
> just everyone needs to understand that it will recognize only a  
> limited number of syntactical variations, and beyond that if you  
> want correct taxon attributes you will a database (be it flatfile,  
> eutil, whatever) lookup.

Aha!  We seem to agree on that...

>> If people want to
>> have reliable $species->species or $species-genus for taxonomy
>> information, they will need to have the db_handle() set for the
>> Bio::Taxonomy::Node object and have an Node-based method to reset
>> species, genus, etc to the tax database information (maybe
>> reset_taxon or something along those lines).
>
> That's what I've saying all along.
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================

I thought you had mentioned something about this a few months back on  
EMBL format issues with organism data.  Anyway, I don't think it was  
from anybody disagreeing with you as much as it was one of the  
project priorities that sort of got lost in the shuffle.  I'm sure  
Sendu will like having a bit of freedom with Bio::Taxonomy::Node.

Anyway, I'll do what I can within reason; I have to leave next  
weekend for a 5-day conference.


Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign