[Bioperl-l] Bio::*Taxonomy* changes (Chris Fields)

[Chris Fields]

On Jul 29, 2006, at 2:54 AM, Sendu Bala wrote:

> Chris Fields wrote:
>>
>> As for branch lengths, I think you're confusing  
>> 'taxonomy' (classification
>> of organisms based on just about anything) with  
>> 'phylogeny' (evolutionary
>> relatedness).  Note in the Wikipedia article below the use of the  
>> term
>> 'phylogenetic taxonomy', which is the classification of organisms  
>> based on
>> evolutionary relationships.
>>
>> http://en.wikipedia.org/wiki/Taxonomy
>>
>> http://en.wikipedia.org/wiki/Phylogeny
>
> Indeed. The two can be considered closely intertwined - if you were
> making a phylogeny you might hang it on a taxonomy. At any rate, you
> need to know a bunch of evolutionarily related species names before  
> you
> start work, and Bio::Taxonomy::Node has been as good a place as any to
> get that.

Intertwined, yes, but not exactly the same.  Hence the NCBI  
disclaimer I mentioned:

How to reference the NCBI taxonomy database

The NCBI taxonomy database is not a primary source for taxonomic or  
phylogenetic information. Furthermore, the database does not follow a  
single taxonomic treatise but rather attempts to incorporate  
phylogenetic and taxonomic knowledge from a variety of sources,  
including the published literature, web-based databases, and the  
advice of sequence submitters and outside taxonomy experts.  
Consequently, the NCBI taxonomy database is not a phylogenetic or  
taxonomic authority and should not be cited as such.


>> There are HOWTOs on tree manipulation, population genetics, and  
>> PAML on the
>> wiki which might be a good start for Bioperl phylogenetic methods:
>>
>> http://www.bioperl.org/wiki/HOWTO:Trees
>
> Which is why the Trees HOWTO talks about taxa, and a number of the
> Taxonomy modules have phylogenetic methods like get_lca. (And why  
> there
> is Bio::Taxonomy::Taxon and Tree.)

Are we still thinking about deprecating those?  I have seen very  
little mention of those modules from the mail list archives, and  
Jason mentioned that Bio::Taxonomy::Taxon hasn't been modified in a  
long time.

> I suppose this is another reason to make Bio::Taxonomy::Node (ne
> Bio::Taxon) implement Bio::Tree::NodeI.
>
> (for these reasons I don't think Gabriel's method isn't best  
> appropriate
> as a script - it's something you might do all the time, as a matter of
> course. If Bio::Taxon wasa Bio::Tree::NodeI you would just do my  
> $tree =
> new Bio::Tree::Tree(-root => $bio_taxon); and blamo, instant
> phylogenetic taxonomy)

Brian already deposited the script (see bioperl-guts).  You could use  
it for the methods, of course noting Gabriel's contribution.

Sounds like a good plan to me ; >

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