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

[Chris Fields]

There was some interest in getting Bio::Species to delegate to
Bio::Taxonomy::Node, so having scientific_name() would help quite a bit
since the name used on the ORGANISM line is the scientific name (well, is
supposed to be; famous last words).  Don't know about SwissProt, EMBL, and
others though...

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Monday, July 17, 2006 2:32 PM
> To: Sendu Bala
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::*Taxonomy* changes
> 
> Yes I think $node->scientific_name() as shorthand would be good to
> have. Same BTW for $node->common_names() (which would return an array).
> 
> 	-hilmar
> 
> On Jul 17, 2006, at 2:09 PM, Sendu Bala wrote:
> 
> > Hilmar Lapp wrote:
> >>> I also plan to make $node->name('scientific', 'sapiens'); set and
> >>> get the node name, [...] users will now find the node name in [...]
> >>> @{$node->name('scientific')}
> >>
> >> BTW NCBI guarantees (well, promises) that there will only be one node
> >> name of class 'scientific'.
> >
> > Yes, which is why I feel the API for name() isn't ideal, but
> > thought it
> > would be best to play along. Would having a new scientific_name()
> > method
> > be better, which gets/sets a single value? Perhaps it could just be a
> > more 'sane' shorthand to setting @{$node->name('scientific')} to a
> > list
> > with only the supplied name, and getting ${$node->name
> > ('scientific')}[0] ?
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> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
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