Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver # Do not use this object directly, rather through the Bio::DB::Taxonomy # interface use Bio::DB::Taxonomy; my $db = new Bio::DB::Taxonomy(-source => 'entrez'); my $taxaid = $db->get_taxaid('Homo sapiens'); A driver for querying NCBI Entrez Taxonomy database.

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/ Email jason-at-bioperl.org Additional contributors names and emails here 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::entrez(); Function: Builds a new Bio::DB::Taxonomy::entrez object Returns : an instance of Bio::DB::Taxonomy::entrez Args : -location => URL to Entrez (if you want to override the default) -params => Hashref of URL params if you want to override the default

get_Taxonomy_Node
Title : get_Taxonomy_Node Usage : my $species = $db->get_Taxonomy_Node(-taxonid => $taxonid) Function: Get a Bio::Taxonomy::Taxon object Returns : Bio::Taxonomy::Taxon object(s) [more than one Args : -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, species, genus, etc) or just a single value which is the taxid.

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 : Array of Strings representing species/node name

Some Get/Setter methods

entrez_url
Title : entrez_url Usage : $obj->entrez_url($newval) Function: Get/set entrez URL Returns : value of entrez url (a scalar) Args : on set, new value (a scalar or undef, optional)

entrez_params
Title : entrez_params Usage : $obj->entrez_params($newval) Function: Get/set entrez params Returns : value of entrez_params (a hashref) Args : on set, new value Hashref

Bio::DB::WebBase methods

proxy_string
Title : proxy_string Usage : my $proxy_string = $self->proxy_string($protocol) Function: Get the proxy string (plus user/pass ) Returns : string Args : protocol ('http' or 'ftp'), default 'http'

proxy
Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy Args : $protocol : an array ref of the protocol(s) to set/get $proxyurl : url of the proxy to use for the specified protocol $username : username (if proxy requires authentication) $password : password (if proxy requires authentication)

authentication
Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass