Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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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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.

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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_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