Provided by: libbio-perl-perl_1.7.2-2_all bug


       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 = 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.


       A driver for querying NCBI Entrez Taxonomy database.


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AUTHOR - Jason Stajich



       Sendu Bala:


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

        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

        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

        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)
                  -name    => string (to query by a taxonomy name: common name,
                                      scientific name, etc)
                  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

        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
        Returns : array of integer ids in list context, one of these in scalar context
        Args    : string representing taxon's name

        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)

        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
        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)

        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
        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'

        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)

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