[Bioperl-l] Taxonomy and entrez

Chris Fields cjfields at uiuc.edu
Mon Sep 4 15:09:42 EDT 2006


...

> # prints 'Brassica rapa subsp.'
> print $species->binomial('FULL');
> # prints 'Brassica rapa subsp. pekinensis'

Sendu,

To most biologists 'binomial' means 'Genus species'.  If we decide to
continue using binomial(), adding an argument to retrieve something that
isn't binomial in nature doesn't make much sense.  The only exception would
be if you are always at the species rank, and that isn't always true for
sequence file organism data.  

Also, since we will eventually get rid of Bio::Species altogether, it
doesn't make much sense to me why you want to promote using binomial(),
which will be deprecated as well.  I'm a little confused: shouldn't we be
promoting use of your new Bio::Taxon-based (DB-based) API for retrieving
taxonomy information instead of using the old Bio::Species-based API?  Or am
I missing something? 

Anyway, there is a method for Bio::Species/Bio::Taxon already in place for
getting the full name: scientific_name(), which will not be deprecated.  The
only way I can think of to retrieve the true 'binomial name' w/o reliance on
the sequence file data would be to traverse the lineage to the species rank
for a node (taxon) and retrieve the scientific_name(), which should always
be 'Genus species'.  I guess you could also use the genus rank and get
something like 'Bacillus sp.'. 

This data wouldn't be a kludge from the sequence file information, which we
are trying to get away from anyway.

Chris




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