/ 
bioperl-1.4
/ Bio::DB::Taxonomy

NAME

Bio::DB::Taxonomy - Access to a taxonomy database

SYNOPSIS

use Bio::DB::Taxonomy;
my $db = new Bio::DB::Taxonomy(-source => 'entrez'); # use NCBI Entrez over HTTP
my $taxaid = $db->get_taxonid('Homo sapiens');

DESCRIPTION

This is a front end module for access to a taxonomy database.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = new Bio::DB::Taxonomy(-source => 'entrez');
Function: Builds a new Bio::DB::Taxonomy object 
Returns : an instance of Bio::DB::Taxonomy
Args    : -source => which database source 'entrez' or 'localfile'

get_Taxonomy_Node

Title   : get_Taxonomy_Node
Usage   : my $species = $db->get_Taxonomy_Node(-taxonid => $taxaid)
Function: Get a Bio::Taxonomy::Taxon object for a taxonid
Returns : Bio::Taxonomy::Taxon object
Args    : -taxonid => taxonomy id (to query by taxonid)
           OR
          -name   => string (to query by a taxonomy name: common name, 
                             species, genus, etc)

get_taxonid

Title   : get_taxonid
Usage   : my $taxonid = $db->get_taxonid('Homo sapiens');
Function: Searches for a taxonid (typically ncbi_taxon_id) 
          based on a query string 
Returns : Integer ID
Args    : String representing species/node name

_load_tax_module

Title   : _load_tax_module
Usage   : *INTERNAL Bio::DB::Taxonomy stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args    :