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

[Chris Fields]

I agree with Hilmar's assessment, not b/c I disagree with your  
definition of scientific name or the reasoning Sendu proposes.  I  
think we are somewhat bound to NCBI's nomenclature for their tax  
database.  If we veer away from NCBI's definition for 'scientific  
name' it will just confuse users and lead to more trouble than it's  
worth, frankly.  If we stick with it then any changes NCBI makes  
should be easier to deal with.

Leaving the scientific_name as NCBI designates it, though it probably  
disagrees with ~99% of the world's textbooks, may be the most  
maintainable solution.

Now, binomial() on the other hand...

Chris

On Jul 17, 2006, at 7:52 PM, Brian Osborne wrote:

> Sendu,
>
> The string "sapiens" is not what a biology textbook would call a  
> scientific
> name. You're going to have to respect decades of convention and have
> scientific_name() return the genus and species name.
>
> Brian O.
>
>
> On 7/17/06 5:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote:
>
>> # I plan on maintaining this; scientific_name() would give you the
>> non-redundant sibling-unique name 'sapiens'. binomial() on a species
>> rank and lower would give you 'Homo sapiens' (presumably grabbing the
>> 'Homo' from the parent node with rank 'genus', or similar).
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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