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

[Chris Fields]

I'll respond to both here:

> Sendu Bala wrote:
>
> One last suggestion for discussion:
> 
> It may be appropriate is to rename Bio::Taxonomy::Node to clarify that
> Node has no particular reliance on or association with Bio::Taxonomy or
> the other modules in Bio/Taxonomy/.
> 
> How about calling it Bio::Taxon?
> 
> It is more obvious what to expect from something called 'Bio::Taxon'
> when you know that it is the new 'Bio::Species': like Bio::Species but
> for any taxon. It also makes the class 'top-level' which I think most
> people are happier using; seems like things in sub-directories are more
> for advanced users.

Hilmar explains the namespace issue with Bioperl more concisely below.

You should still be able to use a Node in a Taxonomy, but then again you
should also be able to use a Taxon in a Taxonomy as well (by definition, a
Taxon is part of a Taxonomy as it is a taxonomic unit).  The whole "looking
at this from a biologist's perspective" thing again...

http://en.wikipedia.org/wiki/Taxon

BTW, what exactly is Bio::Taxonomy::Taxon used for?  Looks like it is used
more for building taxonomic trees that anything, so shouldn't it be moved to
Bio::Tree:Taxon (that name isn't used)?  Then you could use
Bio::Taxonomy::Taxon for your purposes.

See, the only concern I have with using the name Bio::Taxon is people
confusing it with Bio::Taxonomy itself or with Bio::Taxonomy::Taxon.  Though
I agree that the name makes sense for what you want.  

> Hilmar Lapp wrote:
>
> I don't think the top-level or sub-directory matters at all and I
> don't want anybody to get used to the notion that that may imply
> anything (except possibly better thought-out structure for the sub-
> directory level). For instance RichSeq is what all rich annotation
> sequence format parsers return, yet it is in a sub-directory.
> 
> I don't any real objection to Bio::Taxon though if that's what you'd
> like to name it - although, what will happen to the Bio::Taxonomy
> hierarchy then? Phased out?
> 
> 	-hilmar

I'm not sure how many people out there use Bio::Taxonomy.  I think they use
the tree-building modules in Bio::Tree more than anything.  And there
haven't been any panicked users protesting at the gates yet about the many
posts for Bio::Taxonomy changes (well, except me, and 'I got better').  

Chris