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Rutger Vos > Bio-Phylo > Bio::Phylo::PhyloWS::Service::UbioNameBank



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Bio::Phylo::PhyloWS::Service::UbioNameBank - PhyloWS service wrapper for uBio NameBank records


 # inside a CGI script:
 use CGI;
 use Bio::Phylo::PhyloWS::Service::UbioNameBank;

 # obtain a key code from
 # and define it as an environment variable:
 $ENV{'UBIO_KEYCODE'} = '******';
 my $cgi = CGI->new;
 my $service = Bio::Phylo::PhyloWS::Service::UbioNameBank->new( '-base_uri' => $url );


This is an example implementation of a PhyloWS service. The service wraps around some of the uBio XML services described at

Record lookups for this service return project objects that capture the RDF metadata for a single NameBank record as semantic annotations to a taxon object. An example of the sort of metadata that can be expected is shown here:

Queries on this service run namebank searches and return project objects that capture the NameBank search XML (an example is shown here: as semantic annotations to taxon objects.

URLs to this service that specify format=html in the query string redirect to web pages on the uBio site at The redirect URLs either point to search result listings or to NameBank record pages, depending on whether the redirect is for a record query or a record lookup, respectively.


Some functionality of this service requires a key code to the uBio API. Such key codes can be obtained from When deploying this service on a web server (e.g. as shown in the SYNOPSIS) this code must be provided in an environment variable called UBIO_KEYCODE.




Gets a uBio namebank record by its id

 Type    : Accessor
 Title   : get_record
 Usage   : my $record = $obj->get_record( -guid => $guid );
 Function: Gets a uBio namebank record by its id
 Returns : Bio::Phylo::Project
 Args    : Required: -guid => $guid
 Comments: For the $guid argument, this method only cares
           whether the last part of the argument is a series
           of integers, which are understood to be namebank

Gets the authority prefix (e.g. TB2) for the implementing service

 Type    : Authority
 Title   : get_authority
 Usage   : my $auth = $obj->get_authority;
 Function: Gets authority prefix
 Returns : 'uBioNB'
 Args    : None

Gets an array ref of supported formats

 Type    : Accessor
 Title   : get_supported_formats
 Usage   : my @formats = @{ $obj->get_supported_formats };
 Function: Gets an array ref of supported formats
 Returns : [ qw(nexml nexus html json) ]
 Args    : NONE

Gets a redirect URL if relevant

 Type    : Accessor
 Title   : get_redirect
 Usage   : my $url = $obj->get_redirect;
 Function: Gets a redirect URL if relevant
 Returns : String
 Args    : $cgi
 Comments: This method is called by handle_request so that
           services can 303 redirect a record lookup to 
           another URL. By default, this method returns 
           undef (i.e. no redirect), but if this implementation
           is called to handle a request that specifies 
           'format=html' the request is forwarded to the
           appropriate page on the website

Gets a query result and returns it as a project object

 Type    : Accessor
 Title   : get_query_result
 Usage   : my $proj = $obj->get_query_result($query);
 Function: Gets a query result
 Returns : Bio::Phylo::Project
 Args    : A simple query string for a namebank search
 Comments: The $query is a simple CQL level 0 term-only query


There is a mailing list at!forum/bio-phylo for any user or developer questions and discussions.

Also see the manual: Bio::Phylo::Manual and


If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63.

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