NAME

       Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver

SYNOPSIS

       # Do not use this object directly, rather through the Bio::DB::Taxonomy # interface

         use Bio::DB::Taxonomy;

         my $db = Bio::DB::Taxonomy->new(-source => 'entrez');

         my $taxonid = $db->get_taxonid('Homo sapiens');
         my $node   = $db->get_Taxonomy_Node(-taxonid => $taxonid);

         my $gi = 71836523;
         my $node = $db->get_Taxonomy_Node(-gi => $gi, -db => 'protein');
         print $node->binomial, "\n";
         my ($species,$genus,$family) =  $node->classification;
         print "family is $family\n";

         # Can also go up 4 levels
         my $p = $node;
         for ( 1..4 ) {
           $p = $db->get_Taxonomy_Node(-taxonid => $p->parent_id);
         }
         print $p->rank, " ", ($p->classification)[0], "\n";

         # could then classify a set of BLAST hits based on their GI numbers
         # into taxonomic categories.

       It is not currently possibly to query a node for its children so we cannot completely
       replace the advantage of the flatfile Bio::DB::Taxonomy::flatfile module.

DESCRIPTION

       A driver for querying NCBI Entrez 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/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

CONTRIBUTORS

       Sendu Bala: bix@sendu.me.uk

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 = Bio::DB::Taxonomy::entrez->new();
        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_num_taxa
        Title   : get_num_taxa
        Usage   : my $num = $db->get_num_taxa();
        Function: Get the number of taxa stored in the database.
        Returns : A number
        Args    : None

   get_taxon
        Title   : get_taxon
        Usage   : my $taxon = $db->get_taxon(-taxonid => $taxonid)
        Function: Get a Bio::Taxon object from the database.
        Returns : Bio::Taxon object
        Args    : just a single value which is the database id, OR named args:
                  -taxonid => taxonomy id (to query by taxonid)
                   OR
                  -name    => string (to query by a taxonomy name: common name,
                                      scientific name, etc)
                   OR
                  To retrieve a taxonomy node for a GI number provide the -gi option
                  with the gi number and -db with either 'nucleotide' or 'protein' to
                  define the db.
                   AND optionally,
                  -full    => 1 (to force retrieval of full information - sometimes
                                 minimal information about your taxon may have been
                                 cached, which is normally used to save database
                                 accesses)

   get_taxonids
        Title   : get_taxonids
        Usage   : my $taxonid = $db->get_taxonids('Homo sapiens');
        Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query
                  string. Note that multiple taxonids can match to the same supplied
                  name.
        Returns : array of integer ids in list context, one of these in scalar context
        Args    : string representing taxon's name

   ancestor
        Title   : ancestor
        Usage   : my $ancestor_taxon = $db->ancestor($taxon)
        Function: Retrieve the ancestor taxon of a supplied Taxon from the database.

                  Note that unless the ancestor has previously been directly
                  requested with get_taxon(), the returned Taxon object will only have
                  a minimal amount of information.

        Returns : Bio::Taxon
        Args    : Bio::Taxon (that was retrieved from this database)

   each_Descendent
        Title   : each_Descendent
        Usage   : my @taxa = $db->each_Descendent($taxon);
        Function: Get all the descendents of the supplied Taxon (but not their
                  descendents, ie. not a recursive fetchall).

                  Note that this implementation is unable to return a taxon that
                  hasn't previously been directly fetched with get_taxon(), or wasn't
                  an ancestor of such a fetch.

        Returns : Array of Bio::Taxon objects
        Args    : Bio::Taxon (that was retrieved from this database)

   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