[Bioperl-l] taxonomic information handler

[Dan Kortschak]

Forgot to cc to list...

Jason, I can suggest the kinds of things that I would find useful in this
hierarchy (and some things that would be fun) - not sure if this is what
you want, but anyway:


Bio::Taxonomy
	->new ($method)
		argument: $method - NCBI/Entrez or local SQL species tree
		returns: Bio::Taxonomy object

	->get_organism_by_taxid ($taxid)
		argument: taxon id number
		returns: Bio::Species object

	->get_organism_by_name ($name,$mode)
		argument: taxon name, search mode common/Linean/any/et c.
		returns: Bio::Species object

	->get_organism_by_acc ($acc)
		argument: gene accession number
		returns: Bio::Species object

	->get_organism_by_id ($id)
		argument: gene/protein id
		returns: Bio::Species object

	->decendants ($taxid)
		argument: taxon id number
                returns: array of Bio::Tree::SpeciesTree object
		# I'm not sure that the NCBI taxonomy nodes table actually
		# allows this is a reasonable way since links only point
		# towards the root node, but once done the ::Tree objects
		# point downwards.

	::Tree
	# Inherits from Bio::TreeI pretty much the same as
	# Bio::Tree::Tree, but doesn't need branch lengths (maybe, useful
	# for diverence times?)

	::Node
	# Inherits from Bio::NodeI pretty much the same as
	# Bio::Tree::Node, but doesn't need bootstrap et c. (length for
	# divergence time?)
		->description ($species)
                	argument: Bio::Species object
                	returns: Bio::Species object


Since a taxid can be at levels above species, the Bio::Species objects may
be semantically broken (though still functional, since
Bio::Species->classification can hold the appropriate information and
->genus...sub_species can be left undef to reflect this - ->common_name
still useful at the > genus level).

I'd be keen to write some of this, but at the moment my SQL can be
quantified as non-existant (hence my use of arrays in my previous post).
I'd be happy to learn when I have time and do it then though. I guess I'll
have to learn about writing perl objects too :)

cheers
Dan

BTW It has just occured to me that something along the same lines would be
appropriate for the GeneOntology data heirarchy as well. Would this fit
into Bio::Taxonomy?

On Tue, 1 Oct 2002, Jason Stajich wrote:

> I think we would like someone to do the Taxonomy namespace for sure.
>
> I have written a connector to NCBI to retrieve ncbi_taxaid for an organism
> name, its in scripts/taxa.  Would love to be able to populate a whole data
> object as well if we can design one.
>
> Would be great if someone (other than me) would flesh out the
> Bio::Taxonomy objects.  There was a proposed relational structure from
> Matthew that may have made its way a module of the biosql schema.
>
> Dan would you be brave enough to propose a set of objects which relate a
> taxanomic hierarchy?  This might utilize objects such as Bio::Graph but I
> wouldn't worry about that right now.  I would drive this based on use
> cases that you have for taxonomic data.
>
> -jason

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